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