10 20 30 40 50 60 70 80 3FTH - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER PROTEIN FIBRIL 13-JAN-09 3FTH
TITLE NFLVHSS SEGMENT FROM ISLET AMYLOID POLYPEPTIDE (IAPP OR TITLE 2 AMYLIN)
COMPND MOL_ID: 1; COMPND 2 MOLECULE: NFLVHSS HEPTAPEPTIDE FROM ISLET AMYLOID COMPND 3 POLYPEPTIDE; COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PROTEIN IS NATURALLY FOUND IN HOMO SOURCE 4 SAPIENS (HUMAN).
KEYWDS AMYLOID-LIKE PROTOFIBRIL, PROTEIN FIBRIL
EXPDTA X-RAY DIFFRACTION
AUTHOR J.J.W.WILTZIUS,M.R.SAWAYA,D.EISENBERG
REVDAT 3 15-SEP-09 3FTH 1 JRNL REVDAT 2 18-AUG-09 3FTH 1 JRNL REVDAT 1 30-JUN-09 3FTH 0
JRNL AUTH J.J.WILTZIUS,M.LANDAU,R.NELSON,M.R.SAWAYA, JRNL AUTH 2 M.I.APOSTOL,L.GOLDSCHMIDT,A.B.SORIAGA,D.CASCIO, JRNL AUTH 3 K.RAJASHANKAR,D.EISENBERG JRNL TITL MOLECULAR MECHANISMS FOR PROTEIN-ENCODED JRNL TITL 2 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 1
REMARK 2 REMARK 2 RESOLUTION. 1.84 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0061 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 926 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) : 0.242 REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.900 REMARK 3 FREE R VALUE TEST SET COUNT : 101 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.84 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.89 REMARK 3 REFLECTION IN BIN (WORKING SET) : 64 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.61 REMARK 3 BIN R VALUE (WORKING SET) : 0.2550 REMARK 3 BIN FREE R VALUE SET COUNT : 5 REMARK 3 BIN FREE R VALUE : 0.2160 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 124 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 7 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.19 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.19000 REMARK 3 B22 (A**2) : 0.71000 REMARK 3 B33 (A**2) : -0.51000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.10000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.322 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.223 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.108 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.396 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 132 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 76 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 182 ; 1.556 ; 1.981 REMARK 3 BOND ANGLES OTHERS (DEGREES): 190 ; 1.165 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 16 ; 7.686 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 6 ;30.225 ;23.333 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 20 ;13.671 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 22 ; 0.112 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 140 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 28 ; 0.001 ; 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): 76 ; 2.180 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 28 ; 0.581 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 124 ; 3.246 ; 3.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 56 ; 2.367 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 56 ; 3.044 ; 3.000 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 REMARK 3 RIDING POSITIONS
REMARK 4 REMARK 4 3FTH COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JAN-09. REMARK 100 THE RCSB ID CODE IS RCSB051022.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 2 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 : HKL REMARK 200 DATA SCALING SOFTWARE : HKL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 932 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 90.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.18900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.46000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 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 (%): 27.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5M AMMONIUM SULFATE, 0.1 M SODIUM REMARK 280 ACETATE TRIHYDRATE PH 4.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 10.80000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL
REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: THE AUTHORS STATE THAT THE BIOLOGICAL UNIT IS A REMARK 300 INDEFINITELY LONG PAIR OF SHEETS (A PROTOFIBRIL). ONE SHEET REMARK 300 FORMED BY CHAINS A AND B AND THEIR CRYSTALLOGRAPHIC TRANSLATIONS REMARK 300 ALONG THE "A" CELL DIMENSION (E.G. X,Y,Z AND X+1,Y,Z). THE REMARK 300 SECOND SHEET IS CONSTRUCTED FROM -X, Y+1/2,-Z AND THEIR REMARK 300 CRYSTALLOGRAPHIC TRANSLATIONS ALONG THE "A" CELL DIMENSION (E.G. REMARK 300 -X+1, Y+1/2,-Z).
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL 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 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 9.72500 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL 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
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 8
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3FOD RELATED DB: PDB REMARK 900 RELATED ID: 3FPO RELATED DB: PDB REMARK 900 RELATED ID: 3FQP RELATED DB: PDB REMARK 900 RELATED ID: 3FR1 RELATED DB: PDB REMARK 900 RELATED ID: 3FTK RELATED DB: PDB REMARK 900 RELATED ID: 3FTL RELATED DB: PDB
DBREF 3FTH A 1 7 PDB 3FTH 3FTH 1 7 DBREF 3FTH B 1 7 PDB 3FTH 3FTH 1 7
SEQRES 1 A 7 ASN PHE LEU VAL HIS SER SER SEQRES 1 B 7 ASN PHE LEU VAL HIS SER SER
HET SO4 A 8 5
HETNAM SO4 SULFATE ION
FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *6(H2 O)
SHEET 1 A 2 PHE A 2 SER A 6 0 SHEET 2 A 2 PHE B 2 SER B 6 -1 O SER B 6 N PHE A 2
SITE 1 AC1 1 ASN A 1
CRYST1 9.725 21.600 26.086 90.00 95.56 90.00 P 1 21 1 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 0.102828 0.000000 0.010001 0.00000
SCALE2 0.000000 0.046296 0.000000 0.00000
SCALE3 0.000000 0.000000 0.038516 0.00000