HEADER    LIGASE                                  25-MAR-04   1VDX               
TITLE     CRYSTAL STRUCTURE OF A PYROCOCCUS HORIKOSHII PROTEIN WITH SIMILARITIES 
TITLE    2 TO 2'5' RNA-LIGASE                                                    
COMPND    MOL_ID: 1;                                                             
COMPND   2 MOLECULE: HYPOTHETICAL PROTEIN PH0099;                                
COMPND   3 CHAIN: A;                                                             
COMPND   4 SYNONYM: 2'-5' RNA LIGASE RELATED PROTEIN;                            
COMPND   5 EC: 6.5.1.3;                                                          
COMPND   6 ENGINEERED: YES                                                       
SOURCE    MOL_ID: 1;                                                             
SOURCE   2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII;                           
SOURCE   3 ORGANISM_TAXID: 53953;                                                
SOURCE   4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);                        
SOURCE   5 EXPRESSION_SYSTEM_TAXID: 469008;                                      
SOURCE   6 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3);                                 
SOURCE   7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;                               
SOURCE   8 EXPRESSION_SYSTEM_PLASMID: PET-11A                                    
KEYWDS    LIGASE, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN       
KEYWDS   2 STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL                  
KEYWDS   3 GENOMICS/PROTEOMICS INITIATIVE, RSGI                                  
EXPDTA    X-RAY DIFFRACTION                                                      
AUTHOR    P.H.REHSE,T.H.TAHIROV,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE  
AUTHOR   2 (RSGI)                                                                
REVDAT   4   25-OCT-23 1VDX    1       REMARK                                    
REVDAT   3   24-FEB-09 1VDX    1       VERSN                                     
REVDAT   2   14-FEB-06 1VDX    1       JRNL   REMARK                             
REVDAT   1   12-APR-05 1VDX    0                                                 
JRNL        AUTH   P.H.REHSE,T.H.TAHIROV                                         
JRNL        TITL   STRUCTURE OF A PUTATIVE 2'-5' RNA LIGASE FROM PYROCOCCUS      
JRNL        TITL 2 HORIKOSHII.                                                   
JRNL        REF    ACTA CRYSTALLOGR.,SECT.D      V.  61  1207 2005               
JRNL        REFN                   ISSN 0907-4449                                
JRNL        PMID   16131753                                                      
JRNL        DOI    10.1107/S0907444905017841                                     
REMARK   2                                                                       
REMARK   2 RESOLUTION.    2.40 ANGSTROMS.                                        
REMARK   3                                                                       
REMARK   3 REFINEMENT.                                                           
REMARK   3   PROGRAM     : CNS 1.1                                               
REMARK   3   AUTHORS     : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-               
REMARK   3               : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,               
REMARK   3               : READ,RICE,SIMONSON,WARREN                             
REMARK   3                                                                       
REMARK   3  REFINEMENT TARGET : ENGH & HUBER                                     
REMARK   3                                                                       
REMARK   3  DATA USED IN REFINEMENT.                                             
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40                            
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 39.84                           
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000                           
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : 399182.780                      
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : 0.0000                          
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 95.3                            
REMARK   3   NUMBER OF REFLECTIONS             : 7386                            
REMARK   3                                                                       
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                      
REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT                       
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM                           
REMARK   3   R VALUE            (WORKING SET) : 0.225                            
REMARK   3   FREE R VALUE                     : 0.274                            
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 7.500                            
REMARK   3   FREE R VALUE TEST SET COUNT      : 552                              
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : 0.012                            
REMARK   3                                                                       
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.                                   
REMARK   3   TOTAL NUMBER OF BINS USED           : 6                             
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 2.40                          
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.55                          
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 90.40                         
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : 1045                          
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2770                        
REMARK   3   BIN FREE R VALUE                    : 0.3260                        
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : 7.40                          
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : 83                            
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : 0.036                         
REMARK   3                                                                       
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                     
REMARK   3   PROTEIN ATOMS            : 1488                                     
REMARK   3   NUCLEIC ACID ATOMS       : 0                                        
REMARK   3   HETEROGEN ATOMS          : 1                                        
REMARK   3   SOLVENT ATOMS            : 41                                       
REMARK   3                                                                       
REMARK   3  B VALUES.                                                            
REMARK   3   FROM WILSON PLOT           (A**2) : 29.80                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 43.50                           
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                        
REMARK   3    B11 (A**2) : 5.96000                                               
REMARK   3    B22 (A**2) : -2.81000                                              
REMARK   3    B33 (A**2) : -3.16000                                              
REMARK   3    B12 (A**2) : 0.00000                                               
REMARK   3    B13 (A**2) : 0.00000                                               
REMARK   3    B23 (A**2) : 0.00000                                               
REMARK   3                                                                       
REMARK   3  ESTIMATED COORDINATE ERROR.                                          
REMARK   3   ESD FROM LUZZATI PLOT        (A) : 0.31                             
REMARK   3   ESD FROM SIGMAA              (A) : 0.27                             
REMARK   3   LOW RESOLUTION CUTOFF        (A) : 5.00                             
REMARK   3                                                                       
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.                          
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : 0.40                             
REMARK   3   ESD FROM C-V SIGMAA          (A) : 0.31                             
REMARK   3                                                                       
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.                                    
REMARK   3   BOND LENGTHS                 (A) : 0.007                            
REMARK   3   BOND ANGLES            (DEGREES) : 1.400                            
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : 22.90                            
REMARK   3   IMPROPER ANGLES        (DEGREES) : 0.910                            
REMARK   3                                                                       
REMARK   3  ISOTROPIC THERMAL MODEL : RESTRAINED                                 
REMARK   3                                                                       
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA                 
REMARK   3   MAIN-CHAIN BOND              (A**2) : 3.290 ; 1.500                 
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : 4.800 ; 2.000                 
REMARK   3   SIDE-CHAIN BOND              (A**2) : 5.240 ; 2.000                 
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : 7.130 ; 2.500                 
REMARK   3                                                                       
REMARK   3  BULK SOLVENT MODELING.                                               
REMARK   3   METHOD USED : FLAT MODEL                                            
REMARK   3   KSOL        : 0.34                                                  
REMARK   3   BSOL        : 40.31                                                 
REMARK   3                                                                       
REMARK   3  NCS MODEL : NULL                                                     
REMARK   3                                                                       
REMARK   3  NCS RESTRAINTS.                         RMS   SIGMA/WEIGHT           
REMARK   3   GROUP  1  POSITIONAL            (A) : NULL  ; NULL                  
REMARK   3   GROUP  1  B-FACTOR           (A**2) : NULL  ; NULL                  
REMARK   3                                                                       
REMARK   3  PARAMETER FILE  1  : PROTEIN_REP.PARAM                               
REMARK   3  PARAMETER FILE  2  : WATER_REP.PARAM                                 
REMARK   3  PARAMETER FILE  3  : ION.PARAM                                       
REMARK   3  PARAMETER FILE  4  : NULL                                            
REMARK   3  TOPOLOGY FILE  1   : PROTEIN.TOP                                     
REMARK   3  TOPOLOGY FILE  2   : WATER.TOP                                       
REMARK   3  TOPOLOGY FILE  3   : ION.TOP                                         
REMARK   3  TOPOLOGY FILE  4   : NULL                                            
REMARK   3                                                                       
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                       
REMARK   4                                                                       
REMARK   4 1VDX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                          
REMARK 100                                                                       
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-MAR-04.                   
REMARK 100 THE DEPOSITION ID IS D_1000006507.                                    
REMARK 200                                                                       
REMARK 200 EXPERIMENTAL DETAILS                                                  
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                   
REMARK 200  DATE OF DATA COLLECTION        : 02-SEP-03                           
REMARK 200  TEMPERATURE           (KELVIN) : 100                                 
REMARK 200  PH                             : 5.8                                 
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                   
REMARK 200                                                                       
REMARK 200  SYNCHROTRON              (Y/N) : N                                   
REMARK 200  RADIATION SOURCE               : ROTATING ANODE                      
REMARK 200  BEAMLINE                       : NULL                                
REMARK 200  X-RAY GENERATOR MODEL          : RIGAKU RU300                        
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                   
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.5418                              
REMARK 200  MONOCHROMATOR                  : MIRRORS                             
REMARK 200  OPTICS                         : NULL                                
REMARK 200                                                                       
REMARK 200  DETECTOR TYPE                  : IMAGE PLATE                         
REMARK 200  DETECTOR MANUFACTURER          : RIGAKU RAXIS                        
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000                            
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK                           
REMARK 200                                                                       
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 7670                                
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.400                               
REMARK 200  RESOLUTION RANGE LOW       (A) : 50.000                              
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000                               
REMARK 200                                                                       
REMARK 200 OVERALL.                                                              
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.1                                
REMARK 200  DATA REDUNDANCY                : 3.410                               
REMARK 200  R MERGE                    (I) : 0.08000                             
REMARK 200  R SYM                      (I) : NULL                                
REMARK 200   FOR THE DATA SET  : 10.0000                             
REMARK 200                                                                       
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                      
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40                      
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.49                      
REMARK 200  COMPLETENESS FOR SHELL     (%) : 98.5                                
REMARK 200  DATA REDUNDANCY IN SHELL       : 3.33                                
REMARK 200  R MERGE FOR SHELL          (I) : 0.42300                             
REMARK 200  R SYM FOR SHELL            (I) : NULL                                
REMARK 200   FOR SHELL         : 3.360                               
REMARK 200                                                                       
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                               
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT         
REMARK 200 SOFTWARE USED: MOLREP                                                 
REMARK 200 STARTING MODEL: 1IUH.PDB                                              
REMARK 200                                                                       
REMARK 200 REMARK: NULL                                                          
REMARK 280                                                                       
REMARK 280 CRYSTAL                                                               
REMARK 280 SOLVENT CONTENT, VS   (%): 44.30                                      
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21                      
REMARK 280                                                                       
REMARK 280 CRYSTALLIZATION CONDITIONS: MES, PEG 4000, PH 5.8, VAPOR              
REMARK 280  DIFFUSION, SITTING DROP, TEMPERATURE 295K                            
REMARK 290                                                                       
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                             
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21                        
REMARK 290                                                                       
REMARK 290      SYMOP   SYMMETRY                                                 
REMARK 290     NNNMMM   OPERATOR                                                 
REMARK 290       1555   X,Y,Z                                                    
REMARK 290       2555   -X+1/2,-Y,Z+1/2                                          
REMARK 290       3555   -X,Y+1/2,-Z+1/2                                          
REMARK 290       4555   X+1/2,-Y+1/2,-Z                                          
REMARK 290                                                                       
REMARK 290     WHERE NNN -> OPERATOR NUMBER                                      
REMARK 290           MMM -> TRANSLATION VECTOR                                   
REMARK 290                                                                       
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                             
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM              
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY                 
REMARK 290 RELATED MOLECULES.                                                    
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000             
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000             
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000             
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000       22.03400             
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000             
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       46.58550             
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000             
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       22.73550             
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       46.58550             
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       22.03400             
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       22.73550             
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000             
REMARK 290                                                                       
REMARK 290 REMARK: NULL                                                          
REMARK 300                                                                       
REMARK 300 BIOMOLECULE: 1                                                        
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM                 
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN                   
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON                
REMARK 300 BURIED SURFACE AREA.                                                  
REMARK 350                                                                       
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN            
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE                 
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS           
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND                           
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.                                
REMARK 350                                                                       
REMARK 350 BIOMOLECULE: 1                                                        
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC                          
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A                                      
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000             
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000             
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000             
REMARK 500                                                                       
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                          
REMARK 500 SUBTOPIC: TORSION ANGLES                                              
REMARK 500                                                                       
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:             
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;                
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                              
REMARK 500                                                                       
REMARK 500 STANDARD TABLE:                                                       
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)                     
REMARK 500                                                                       
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-            
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400             
REMARK 500                                                                       
REMARK 500  M RES CSSEQI        PSI       PHI                                    
REMARK 500    LYS A  44      121.07   -177.19                                    
REMARK 500    ASN A  96      104.51     61.81                                    
REMARK 500    PHE A 133      145.05   -178.51                                    
REMARK 500    PRO A 169      -75.93    -19.45                                    
REMARK 500    SER A 183     -168.40    -70.31                                    
REMARK 500                                                                       
REMARK 500 REMARK: NULL                                                          
REMARK 900                                                                       
REMARK 900 RELATED ENTRIES                                                       
REMARK 900 RELATED ID: PHO000099   RELATED DB: TARGETDB                          
DBREF  1VDX A    1   184  UNP    O57823   Y099_PYRHO       1    184              
SEQRES   1 A  184  MET ARG ALA PHE ILE ALA ILE ASP VAL ASN GLU SER VAL           
SEQRES   2 A  184  ARG ASP SER LEU VAL ARG ALA GLN ASP TYR ILE GLY SER           
SEQRES   3 A  184  LYS GLU ALA LYS ILE LYS PHE VAL GLU ARG GLU ASN LEU           
SEQRES   4 A  184  HIS ILE THR LEU LYS PHE LEU GLY GLU ILE THR GLU GLU           
SEQRES   5 A  184  GLN ALA GLU GLU ILE LYS ASN ILE LEU LYS LYS ILE ALA           
SEQRES   6 A  184  GLU LYS TYR LYS LYS HIS GLU VAL LYS VAL LYS GLY ILE           
SEQRES   7 A  184  GLY VAL PHE PRO ASN PRO ASN TYR ILE ARG VAL ILE TRP           
SEQRES   8 A  184  ALA GLY ILE GLU ASN ASP GLU ILE ILE ARG GLU MET ALA           
SEQRES   9 A  184  ARG GLU ILE GLU ASP GLU LEU ALA LYS LEU GLY PHE LYS           
SEQRES  10 A  184  LYS GLU GLY ASN PHE VAL ALA HIS ILE THR LEU GLY ARG           
SEQRES  11 A  184  VAL LYS PHE VAL LYS ASP LYS LEU GLY LEU THR MET LYS           
SEQRES  12 A  184  LEU LYS GLU LEU ALA ASN GLU ASP PHE GLY SER PHE VAL           
SEQRES  13 A  184  VAL ASP ALA ILE GLU LEU LYS LYS SER THR LEU THR PRO           
SEQRES  14 A  184  LYS GLY PRO ILE TYR GLU THR LEU ALA ARG PHE GLU LEU           
SEQRES  15 A  184  SER GLU                                                       
HET     CL  A 185       1                                                        
HETNAM      CL CHLORIDE ION                                                      
FORMUL   2   CL    CL 1-                                                         
FORMUL   3  HOH   *41(H2 O)                                                      
HELIX    1   1 ASN A   10  GLY A   25  1                                  16     
HELIX    2   2 GLU A   35  ASN A   38  5                                   4     
HELIX    3   3 THR A   50  GLU A   66  1                                  17     
HELIX    4   4 ASP A   97  LYS A  113  1                                  17     
HELIX    5   5 ASP A  136  GLU A  146  1                                  11     
SHEET    1   A 4 HIS A  40  GLU A  48  0                                         
SHEET    2   A 4 ARG A   2  ASP A   8 -1  N  ILE A   5   O  LEU A  43            
SHEET    3   A 4 ALA A 159  THR A 168 -1  O  LYS A 163   N  PHE A   4            
SHEET    4   A 4 GLY A 171  GLU A 181 -1  O  ILE A 173   N  THR A 166            
SHEET    1   B 5 ALA A  29  PHE A  33  0                                         
SHEET    2   B 5 HIS A 125  VAL A 134 -1  O  ARG A 130   N  LYS A  32            
SHEET    3   B 5 ILE A  87  GLU A  95 -1  N  ILE A  90   O  GLY A 129            
SHEET    4   B 5 HIS A  71  PRO A  82 -1  N  LYS A  74   O  GLU A  95            
SHEET    5   B 5 ASP A 151  VAL A 157 -1  O  GLY A 153   N  VAL A  75            
CISPEP   1 PHE A   81    PRO A   82          0        -3.00                      
CRYST1   44.068   45.471   93.171  90.00  90.00  90.00 P 21 21 21    4           
ORIGX1      1.000000  0.000000  0.000000        0.00000                          
ORIGX2      0.000000  1.000000  0.000000        0.00000                          
ORIGX3      0.000000  0.000000  1.000000        0.00000                          
SCALE1      0.022692  0.000000  0.000000        0.00000                          
SCALE2      0.000000  0.021992  0.000000        0.00000                          
SCALE3      0.000000  0.000000  0.010733        0.00000                          
END