HEADER PROTEIN FIBRIL 13-JAN-09 3FTR TITLE STRUCTURE OF AN AMYLOID FORMING PEPTIDE SSTNVG FROM IAPP (ALTERNATE TITLE 2 POLYMORPH) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SSTNVG FROM ISLET AMYLOID POLYPEPTIDE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS AMYLOID-LIKE PROTOFIBRIL, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR M.LANDAU,D.EISENBERG REVDAT 5 21-FEB-24 3FTR 1 REMARK REVDAT 4 01-NOV-17 3FTR 1 REMARK REVDAT 3 15-SEP-09 3FTR 1 JRNL REVDAT 2 18-AUG-09 3FTR 1 JRNL AUTHOR REVDAT 1 30-JUN-09 3FTR 0 JRNL AUTH J.J.WILTZIUS,M.LANDAU,R.NELSON,M.R.SAWAYA,M.I.APOSTOL, JRNL AUTH 2 L.GOLDSCHMIDT,A.B.SORIAGA,D.CASCIO,K.RAJASHANKAR,D.EISENBERG JRNL TITL MOLECULAR MECHANISMS FOR PROTEIN-ENCODED INHERITANCE. JRNL REF NAT.STRUCT.MOL.BIOL. V. 16 973 2009 JRNL REFN ISSN 1545-9993 JRNL PMID 19684598 JRNL DOI 10.1038/NSMB.1643 REMARK 2 REMARK 2 RESOLUTION. 1.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 3 NUMBER OF REFLECTIONS : 486 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 + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 48 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.61 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 101 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.19 REMARK 3 BIN R VALUE (WORKING SET) : 0.2650 REMARK 3 BIN FREE R VALUE SET COUNT : 11 REMARK 3 BIN FREE R VALUE : 0.3960 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 39 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 3 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.97000 REMARK 3 B22 (A**2) : -1.31000 REMARK 3 B33 (A**2) : 0.34000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.150 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.134 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.069 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.990 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.933 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 38 ; 0.004 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 20 ; 0.007 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 51 ; 0.913 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): 51 ; 0.593 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 5 ; 4.121 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 1 ;41.332 ;30.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 5 ; 7.329 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 7 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 43 ; 0.001 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 5 ; 0.000 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 29 ; 1.740 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 12 ; 0.407 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 46 ; 2.574 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 9 ; 1.272 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 5 ; 1.786 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3FTR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000051031. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 503 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 90.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.14900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.4620 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.49900 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR CONTAINED 20% W/V PEG-3000, REMARK 280 0.1M HEPES, 0.2M NACL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K 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 8.29500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 20.11450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 2.39450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 20.11450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 8.29500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 2.39450 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: TETRAMERIC 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -9.57800 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 -4.78900 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 4.78900 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DG1 RELATED DB: PDB REMARK 900 ALTERNATIVE POLYMORPH DBREF 3FTR A 1 6 PDB 3FTR 3FTR 1 6 SEQRES 1 A 6 SER SER THR ASN VAL GLY FORMUL 2 HOH *3(H2 O) CRYST1 16.590 4.789 40.229 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 0.060277 0.000000 0.000000 0.00000 SCALE2 0.000000 0.208812 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024858 0.00000 ATOM 1 N SER A 1 4.969 -1.277 1.460 1.00 14.73 N ATOM 2 CA SER A 1 5.279 -0.549 0.196 1.00 14.65 C ATOM 3 C SER A 1 4.658 -1.245 -1.003 1.00 14.53 C ATOM 4 O SER A 1 4.332 -2.433 -0.944 1.00 14.88 O ATOM 5 CB SER A 1 6.791 -0.440 -0.010 1.00 14.86 C ATOM 6 OG SER A 1 7.397 -1.718 -0.032 1.00 15.12 O ATOM 7 N SER A 2 4.502 -0.501 -2.094 1.00 11.96 N ATOM 8 CA SER A 2 3.978 -1.075 -3.325 1.00 11.53 C ATOM 9 C SER A 2 4.557 -0.400 -4.560 1.00 9.57 C ATOM 10 O SER A 2 4.741 0.821 -4.592 1.00 8.60 O ATOM 11 CB SER A 2 2.449 -1.003 -3.351 1.00 12.49 C ATOM 12 OG SER A 2 1.996 0.315 -3.603 1.00 14.27 O ATOM 13 N THR A 3 4.843 -1.216 -5.570 1.00 6.43 N ATOM 14 CA THR A 3 5.294 -0.742 -6.866 1.00 7.08 C ATOM 15 C THR A 3 4.376 -1.327 -7.935 1.00 5.02 C ATOM 16 O THR A 3 4.273 -2.544 -8.054 1.00 8.36 O ATOM 17 CB THR A 3 6.728 -1.201 -7.148 1.00 6.99 C ATOM 18 OG1 THR A 3 7.586 -0.780 -6.078 1.00 6.97 O ATOM 19 CG2 THR A 3 7.222 -0.632 -8.472 1.00 7.74 C ATOM 20 N ASN A 4 3.723 -0.457 -8.704 1.00 3.28 N ATOM 21 CA ASN A 4 2.790 -0.865 -9.757 1.00 3.84 C ATOM 22 C ASN A 4 3.229 -0.291 -11.090 1.00 3.24 C ATOM 23 O ASN A 4 3.368 0.928 -11.214 1.00 6.03 O ATOM 24 CB ASN A 4 1.388 -0.329 -9.459 1.00 5.00 C ATOM 25 CG ASN A 4 0.771 -0.943 -8.218 1.00 5.57 C ATOM 26 OD1 ASN A 4 0.866 -2.147 -7.991 1.00 6.29 O ATOM 27 ND2 ASN A 4 0.107 -0.114 -7.417 1.00 8.11 N ATOM 28 N VAL A 5 3.446 -1.154 -12.079 1.00 3.03 N ATOM 29 CA VAL A 5 3.776 -0.712 -13.432 1.00 3.55 C ATOM 30 C VAL A 5 2.692 -1.197 -14.371 1.00 3.58 C ATOM 31 O VAL A 5 2.486 -2.400 -14.513 1.00 5.58 O ATOM 32 CB VAL A 5 5.126 -1.255 -13.915 1.00 6.04 C ATOM 33 CG1 VAL A 5 5.403 -0.764 -15.327 1.00 7.70 C ATOM 34 CG2 VAL A 5 6.227 -0.820 -12.973 1.00 6.88 C ATOM 35 N GLY A 6 2.000 -0.259 -15.008 1.00 7.44 N ATOM 36 CA GLY A 6 0.861 -0.591 -15.855 1.00 9.48 C ATOM 37 C GLY A 6 1.272 -1.366 -17.088 1.00 11.54 C ATOM 38 O GLY A 6 2.425 -1.297 -17.521 1.00 11.27 O ATOM 39 OXT GLY A 6 0.456 -2.076 -17.677 1.00 13.21 O TER 40 GLY A 6 HETATM 41 O HOH A 7 7.544 1.577 -4.361 1.00 9.77 O HETATM 42 O HOH A 8 9.013 -2.709 -1.942 1.00 23.92 O HETATM 43 O HOH A 9 -1.450 -1.522 -19.336 1.00 32.99 O MASTER 248 0 0 0 0 0 0 6 42 1 0 1 END