HEADER UNKNOWN FUNCTION 31-MAY-18 6DKY TITLE CRYSTAL STRUCTURE OF RIBIFOLIN, AN ORBITIDE FROM JATROPHA RIBIFOLIA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ILE-LEU-GLY-SER-ILE-ILE-LEU-GLY; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: JATROPHA; SOURCE 4 ORGANISM_TAXID: 3995 KEYWDS CYCLIC PEPTIDE, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR C.K.WANG,S.D.RAMALHO,G.J.KING,D.J.CRAIK REVDAT 4 20-NOV-24 6DKY 1 LINK REVDAT 3 01-JAN-20 6DKY 1 LINK REVDAT 2 05-DEC-18 6DKY 1 JRNL REVDAT 1 07-NOV-18 6DKY 0 JRNL AUTH S.D.RAMALHO,C.K.WANG,G.J.KING,K.A.BYRIEL,Y.H.HUANG, JRNL AUTH 2 V.S.BOLZANI,D.J.CRAIK JRNL TITL SYNTHESIS, RACEMIC X-RAY CRYSTALLOGRAPHIC, AND PERMEABILITY JRNL TITL 2 STUDIES OF BIOACTIVE ORBITIDES FROM JATROPHA SPECIES. JRNL REF J. NAT. PROD. V. 81 2436 2018 JRNL REFN ESSN 1520-6025 JRNL PMID 30345754 JRNL DOI 10.1021/ACS.JNATPROD.8B00447 REMARK 2 REMARK 2 RESOLUTION. 1.24 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2142: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 3327 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 336 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.1443 - 1.5613 1.00 1546 170 0.1980 0.2217 REMARK 3 2 1.5613 - 1.2393 0.99 1445 166 0.1921 0.2250 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.019 108 REMARK 3 ANGLE : 1.689 140 REMARK 3 CHIRALITY : 0.132 22 REMARK 3 PLANARITY : 0.008 14 REMARK 3 DIHEDRAL : 7.445 36 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6DKY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000234830. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3333 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.239 REMARK 200 RESOLUTION RANGE LOW (A) : 16.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 11.90 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.24 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.28 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.22400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SHELXCD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS BASE (PH 8.0) AND 40% 2 REMARK 280 -METHYL-2,4-PENTANEDIOL (MPD), VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 11.81600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 11.92550 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 11.81600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 11.92550 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 DBREF 6DKY A 6 5 PDB 6DKY 6DKY 6 5 DBREF 6DKY B 6 5 PDB 6DKY 6DKY 6 5 SEQRES 1 A 8 ILE LEU GLY SER ILE ILE LEU GLY SEQRES 1 B 8 ILE LEU GLY SER ILE ILE LEU GLY FORMUL 3 HOH *2(H2 O) LINK C GLY A 5 N ILE A 6 1555 1555 1.32 LINK C GLY B 5 N ILE B 6 1555 1555 1.32 CRYST1 19.142 23.632 23.851 90.00 90.00 90.00 P 2 21 21 8 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 0.052241 0.000000 0.000000 0.00000 SCALE2 0.000000 0.042316 0.000000 0.00000 SCALE3 0.000000 0.000000 0.041927 0.00000 ATOM 1 N ILE A 6 -15.631 5.869 10.035 1.00 7.21 N ATOM 2 CA ILE A 6 -14.293 5.572 10.523 1.00 7.20 C ATOM 3 C ILE A 6 -13.604 4.843 9.394 1.00 7.05 C ATOM 4 O ILE A 6 -14.252 4.503 8.404 1.00 6.73 O ATOM 5 CB ILE A 6 -14.319 4.720 11.814 1.00 7.65 C ATOM 6 CG1 ILE A 6 -15.041 3.415 11.566 1.00 7.58 C ATOM 7 CG2 ILE A 6 -14.925 5.487 12.992 1.00 9.16 C ATOM 8 CD1 ILE A 6 -14.786 2.381 12.645 1.00 9.04 C ATOM 9 N LEU A 7 -12.310 4.558 9.558 1.00 6.73 N ATOM 10 CA LEU A 7 -11.533 3.769 8.601 1.00 7.80 C ATOM 11 C LEU A 7 -11.578 4.354 7.187 1.00 7.01 C ATOM 12 O LEU A 7 -11.446 3.619 6.197 1.00 7.43 O ATOM 13 CB LEU A 7 -11.935 2.283 8.618 1.00 7.45 C ATOM 14 CG LEU A 7 -11.601 1.554 9.924 1.00 8.17 C ATOM 15 CD1 LEU A 7 -12.225 0.202 9.894 1.00 10.40 C ATOM 16 CD2 LEU A 7 -10.116 1.356 10.127 1.00 9.31 C ATOM 17 N GLY A 8 -11.769 5.667 7.089 1.00 5.93 N ATOM 18 CA GLY A 8 -11.764 6.312 5.797 1.00 7.54 C ATOM 19 C GLY A 8 -12.998 6.033 4.974 1.00 6.75 C ATOM 20 O GLY A 8 -12.963 6.199 3.759 1.00 8.20 O ATOM 21 N SER A 1 -14.056 5.605 5.589 1.00 6.54 N ATOM 22 CA SER A 1 -15.305 5.292 4.902 1.00 6.85 C ATOM 23 C SER A 1 -16.435 6.263 5.233 1.00 6.54 C ATOM 24 O SER A 1 -16.734 6.517 6.347 1.00 6.28 O ATOM 25 CB SER A 1 -15.746 3.875 5.307 1.00 7.96 C ATOM 26 OG SER A 1 -17.122 3.587 5.046 1.00 9.36 O ATOM 27 N ILE A 2 -17.120 6.725 4.206 1.00 6.30 N ATOM 28 CA ILE A 2 -18.328 7.593 4.299 1.00 8.44 C ATOM 29 C ILE A 2 -19.428 6.913 5.049 1.00 6.22 C ATOM 30 O ILE A 2 -20.111 7.527 5.765 1.00 8.52 O ATOM 31 CB ILE A 2 -18.913 7.936 2.836 1.00 10.20 C ATOM 32 CG1 ILE A 2 -17.933 8.829 2.127 1.00 12.89 C ATOM 33 CG2 ILE A 2 -20.273 8.643 2.930 1.00 11.19 C ATOM 34 CD1 ILE A 2 -18.481 9.432 0.833 1.00 14.56 C ATOM 35 N ILE A 3 -19.591 5.639 4.788 1.00 7.44 N ATOM 36 CA ILE A 3 -20.697 4.913 5.444 1.00 8.22 C ATOM 37 C ILE A 3 -20.415 4.687 6.944 1.00 6.71 C ATOM 38 O ILE A 3 -21.265 4.806 7.732 1.00 6.98 O ATOM 39 CB ILE A 3 -21.013 3.575 4.730 1.00 11.61 C ATOM 40 CG1 ILE A 3 -21.518 3.884 3.338 1.00 18.03 C ATOM 41 CG2 ILE A 3 -22.039 2.757 5.527 1.00 16.02 C ATOM 42 CD1 ILE A 3 -21.887 2.698 2.515 1.00 20.10 C ATOM 43 N LEU A 4 -19.194 4.269 7.267 1.00 6.83 N ATOM 44 CA LEU A 4 -18.851 3.933 8.691 1.00 7.61 C ATOM 45 C LEU A 4 -18.482 5.120 9.537 1.00 7.16 C ATOM 46 O LEU A 4 -18.537 5.052 10.736 1.00 7.66 O ATOM 47 CB LEU A 4 -17.714 2.922 8.737 1.00 8.58 C ATOM 48 CG LEU A 4 -17.975 1.580 8.070 1.00 8.93 C ATOM 49 CD1 LEU A 4 -16.726 0.696 8.240 1.00 10.93 C ATOM 50 CD2 LEU A 4 -19.190 0.821 8.584 1.00 12.17 C ATOM 51 N GLY A 5 -18.065 6.200 8.891 1.00 6.69 N ATOM 52 CA GLY A 5 -17.556 7.309 9.641 1.00 8.10 C ATOM 53 C GLY A 5 -16.244 7.005 10.330 1.00 8.38 C ATOM 54 O GLY A 5 -15.769 7.844 11.100 1.00 10.17 O TER 55 GLY A 5 ATOM 56 N ILE B 6 -25.304 6.626 7.460 1.00 5.74 N ATOM 57 CA ILE B 6 -23.992 6.963 6.969 1.00 7.09 C ATOM 58 C ILE B 6 -23.240 7.612 8.108 1.00 6.84 C ATOM 59 O ILE B 6 -23.829 7.870 9.155 1.00 6.23 O ATOM 60 CB ILE B 6 -24.029 7.882 5.708 1.00 8.44 C ATOM 61 CG1 ILE B 6 -24.621 9.234 6.058 1.00 8.79 C ATOM 62 CG2 ILE B 6 -24.731 7.205 4.539 1.00 10.57 C ATOM 63 CD1 ILE B 6 -24.454 10.246 4.992 1.00 10.64 C ATOM 64 N LEU B 7 -21.940 7.832 7.904 1.00 6.87 N ATOM 65 CA LEU B 7 -21.095 8.510 8.867 1.00 8.12 C ATOM 66 C LEU B 7 -21.135 7.814 10.227 1.00 6.19 C ATOM 67 O LEU B 7 -21.002 8.452 11.284 1.00 7.76 O ATOM 68 CB LEU B 7 -21.431 10.005 8.986 1.00 9.58 C ATOM 69 CG LEU B 7 -21.315 10.778 7.663 1.00 11.43 C ATOM 70 CD1 LEU B 7 -21.890 12.196 7.728 1.00 13.96 C ATOM 71 CD2 LEU B 7 -19.847 10.792 7.235 1.00 12.80 C ATOM 72 N GLY B 8 -21.329 6.495 10.227 1.00 6.07 N ATOM 73 CA GLY B 8 -21.332 5.749 11.477 1.00 8.04 C ATOM 74 C GLY B 8 -22.483 6.049 12.408 1.00 7.24 C ATOM 75 O GLY B 8 -22.351 5.831 13.623 1.00 8.79 O ATOM 76 N SER B 1 -23.608 6.488 11.875 1.00 6.01 N ATOM 77 CA SER B 1 -24.801 6.777 12.647 1.00 6.72 C ATOM 78 C SER B 1 -25.930 5.862 12.207 1.00 7.58 C ATOM 79 O SER B 1 -26.243 5.788 11.013 1.00 6.20 O ATOM 80 CB SER B 1 -25.216 8.235 12.456 1.00 7.57 C ATOM 81 OG SER B 1 -26.562 8.445 12.888 1.00 8.96 O ATOM 82 N ILE B 2 -26.565 5.172 13.157 1.00 6.74 N ATOM 83 CA ILE B 2 -27.674 4.325 12.748 1.00 8.21 C ATOM 84 C ILE B 2 -28.886 5.141 12.384 1.00 6.21 C ATOM 85 O ILE B 2 -29.746 4.611 11.699 1.00 8.11 O ATOM 86 CB ILE B 2 -28.011 3.151 13.666 1.00 10.64 C ATOM 87 CG1 ILE B 2 -28.453 3.737 14.965 1.00 12.15 C ATOM 88 CG2 ILE B 2 -26.856 2.108 13.770 1.00 14.91 C ATOM 89 CD1 ILE B 2 -29.148 2.727 15.844 1.00 14.24 C ATOM 90 N ILE B 3 -28.954 6.402 12.794 1.00 6.51 N ATOM 91 CA ILE B 3 -30.030 7.283 12.364 1.00 8.50 C ATOM 92 C ILE B 3 -29.833 7.729 10.911 1.00 7.93 C ATOM 93 O ILE B 3 -30.729 7.572 10.069 1.00 8.50 O ATOM 94 CB ILE B 3 -30.146 8.460 13.344 1.00 10.44 C ATOM 95 CG1 ILE B 3 -30.495 7.941 14.738 1.00 12.42 C ATOM 96 CG2 ILE B 3 -31.163 9.504 12.843 1.00 13.59 C ATOM 97 CD1 ILE B 3 -30.520 9.020 15.772 1.00 19.07 C ATOM 98 N LEU B 4 -28.642 8.247 10.586 1.00 7.16 N ATOM 99 CA LEU B 4 -28.373 8.727 9.233 1.00 7.73 C ATOM 100 C LEU B 4 -28.196 7.597 8.228 1.00 6.52 C ATOM 101 O LEU B 4 -28.410 7.818 7.033 1.00 7.54 O ATOM 102 CB LEU B 4 -27.122 9.610 9.232 1.00 8.32 C ATOM 103 CG LEU B 4 -27.092 10.800 10.211 1.00 8.78 C ATOM 104 CD1 LEU B 4 -25.775 11.580 10.074 1.00 10.75 C ATOM 105 CD2 LEU B 4 -28.314 11.701 10.071 1.00 11.25 C ATOM 106 N GLY B 5 -27.734 6.421 8.664 1.00 6.50 N ATOM 107 CA GLY B 5 -27.337 5.349 7.794 1.00 7.32 C ATOM 108 C GLY B 5 -25.949 5.505 7.199 1.00 7.48 C ATOM 109 O GLY B 5 -25.518 4.672 6.379 1.00 9.84 O TER 110 GLY B 5 HETATM 111 O HOH A 101 -10.960 0.880 5.237 1.00 19.10 O HETATM 112 O HOH B 101 -29.292 10.785 6.251 1.00 21.21 O CONECT 1 53 CONECT 53 1 CONECT 56 108 CONECT 108 56 MASTER 189 0 0 0 0 0 0 6 110 2 4 2 END