HEADER PROTEIN FIBRIL 05-JAN-09 3FPO TITLE HSSNNF SEGMENT FROM ISLET AMYLOID POLYPEPTIDE (IAPP OR AMYLIN) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HSSNNF HEXAPEPTIDE SEGMENT FROM ISLET AMYLOID POLYPEPTIDE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: HSSNNF (RESIDUES 18-23) FROM HUMAN ISLET AMYLOID SOURCE 4 POLYPEPTIDE, SYNTHESIZED KEYWDS AMYLOID-LIKE PROTOFIBRIL, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR J.J.W.WILTZIUS,M.R.SAWAYA,D.EISENBERG REVDAT 5 21-FEB-24 3FPO 1 REMARK REVDAT 4 01-NOV-17 3FPO 1 REMARK REVDAT 3 15-SEP-09 3FPO 1 JRNL REVDAT 2 18-AUG-09 3FPO 1 JRNL AUTHOR REVDAT 1 30-JUN-09 3FPO 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. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 562 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) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.154 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.400 REMARK 3 FREE R VALUE TEST SET COUNT : 53 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.68 REMARK 3 REFLECTION IN BIN (WORKING SET) : 126 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 77.22 REMARK 3 BIN R VALUE (WORKING SET) : 0.2040 REMARK 3 BIN FREE R VALUE SET COUNT : 13 REMARK 3 BIN FREE R VALUE : 0.2120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 50 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 4 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 5.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.40000 REMARK 3 B22 (A**2) : 0.88000 REMARK 3 B33 (A**2) : -0.48000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.06000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.095 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.080 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.046 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.327 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.979 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 51 ; 0.004 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 30 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 68 ; 0.703 ; 1.796 REMARK 3 BOND ANGLES OTHERS (DEGREES): 72 ; 0.535 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 5 ; 3.153 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 4 ;57.475 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 6 ; 5.176 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 6 ; 0.076 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 60 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 12 ; 0.000 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3 ; 0.146 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 13 ; 0.200 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 21 ; 0.171 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 27 ; 0.070 ; 0.200 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): 5 ; 0.120 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 8 ; 0.184 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.066 ; 0.200 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): 35 ; 0.888 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 11 ; 0.142 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 47 ; 1.596 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 26 ; 1.065 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 21 ; 1.049 ; 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 3FPO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000050886. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 : 568 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 93.6 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.15900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5050 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.57200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: 8% PEG 8000, 0.1M TRIS-HCL, PH 8.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, 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 8.19550 REMARK 290 SMTRY3 2 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 -4.82200 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 BIOMT1 3 1.000000 0.000000 0.000000 4.82200 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 -9.64400 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DGJ RELATED DB: PDB REMARK 900 NNFGAIL,ANOTHER SEGMENT FROM IAPP REMARK 900 RELATED ID: 3DG1 RELATED DB: PDB REMARK 900 SSTNVG, ANOTHER SEGMENT FROM IAPP DBREF 3FPO A 1 6 PDB 3FPO 3FPO 1 6 SEQRES 1 A 6 HIS SER SER ASN ASN PHE FORMUL 2 HOH *4(H2 O) CRYST1 4.822 16.391 23.476 90.00 92.50 90.00 P 1 21 1 2 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 0.207383 0.000000 0.009036 0.00000 SCALE2 0.000000 0.061009 0.000000 0.00000 SCALE3 0.000000 0.000000 0.042637 0.00000 ATOM 1 N HIS A 1 1.742 0.539 -10.091 1.00 2.74 N ATOM 2 CA HIS A 1 0.944 0.193 -8.877 1.00 3.47 C ATOM 3 C HIS A 1 1.665 0.652 -7.616 1.00 3.27 C ATOM 4 O HIS A 1 2.891 0.739 -7.594 1.00 3.07 O ATOM 5 CB HIS A 1 0.691 -1.315 -8.802 1.00 3.90 C ATOM 6 CG HIS A 1 0.084 -1.893 -10.044 1.00 3.79 C ATOM 7 ND1 HIS A 1 -1.028 -1.351 -10.652 1.00 4.46 N ATOM 8 CD2 HIS A 1 0.427 -2.973 -10.785 1.00 4.43 C ATOM 9 CE1 HIS A 1 -1.338 -2.068 -11.717 1.00 4.45 C ATOM 10 NE2 HIS A 1 -0.473 -3.060 -11.818 1.00 4.43 N ATOM 11 N SER A 2 0.902 0.941 -6.566 1.00 3.31 N ATOM 12 CA SER A 2 1.492 1.355 -5.292 1.00 3.92 C ATOM 13 C SER A 2 0.777 0.729 -4.100 1.00 3.19 C ATOM 14 O SER A 2 -0.451 0.622 -4.082 1.00 3.36 O ATOM 15 CB SER A 2 1.500 2.876 -5.165 1.00 4.84 C ATOM 16 OG SER A 2 0.208 3.407 -5.359 1.00 7.94 O ATOM 17 N SER A 3 1.563 0.298 -3.117 1.00 2.89 N ATOM 18 CA SER A 3 1.029 -0.282 -1.889 1.00 3.33 C ATOM 19 C SER A 3 1.571 0.481 -0.684 1.00 2.75 C ATOM 20 O SER A 3 2.730 0.908 -0.672 1.00 2.95 O ATOM 21 CB SER A 3 1.390 -1.764 -1.781 1.00 4.63 C ATOM 22 OG SER A 3 2.792 -1.937 -1.742 1.00 6.72 O ATOM 23 N ASN A 4 0.718 0.639 0.320 1.00 2.75 N ATOM 24 CA ASN A 4 1.030 1.407 1.520 1.00 2.83 C ATOM 25 C ASN A 4 0.527 0.639 2.735 1.00 3.49 C ATOM 26 O ASN A 4 -0.670 0.343 2.831 1.00 4.19 O ATOM 27 CB ASN A 4 0.370 2.779 1.441 1.00 3.45 C ATOM 28 CG ASN A 4 0.719 3.516 0.161 1.00 3.76 C ATOM 29 OD1 ASN A 4 1.790 4.113 0.052 1.00 4.65 O ATOM 30 ND2 ASN A 4 -0.177 3.462 -0.824 1.00 4.75 N ATOM 31 N ASN A 5 1.442 0.301 3.641 1.00 2.95 N ATOM 32 CA ASN A 5 1.125 -0.530 4.806 1.00 3.05 C ATOM 33 C ASN A 5 1.572 0.150 6.098 1.00 3.25 C ATOM 34 O ASN A 5 2.764 0.395 6.286 1.00 4.19 O ATOM 35 CB ASN A 5 1.802 -1.890 4.673 1.00 3.19 C ATOM 36 CG ASN A 5 1.442 -2.592 3.385 1.00 3.53 C ATOM 37 OD1 ASN A 5 0.307 -3.032 3.202 1.00 6.20 O ATOM 38 ND2 ASN A 5 2.405 -2.692 2.475 1.00 4.34 N ATOM 39 N PHE A 6 0.607 0.450 6.970 1.00 3.65 N ATOM 40 CA PHE A 6 0.853 1.139 8.241 1.00 5.17 C ATOM 41 C PHE A 6 0.404 0.265 9.419 1.00 7.73 C ATOM 42 O PHE A 6 0.046 -0.909 9.263 1.00 9.81 O ATOM 43 CB PHE A 6 0.094 2.467 8.289 1.00 4.59 C ATOM 44 CG PHE A 6 0.407 3.403 7.151 1.00 4.22 C ATOM 45 CD1 PHE A 6 -0.325 3.354 5.968 1.00 3.96 C ATOM 46 CD2 PHE A 6 1.412 4.353 7.271 1.00 3.77 C ATOM 47 CE1 PHE A 6 -0.052 4.224 4.921 1.00 3.51 C ATOM 48 CE2 PHE A 6 1.694 5.224 6.230 1.00 4.91 C ATOM 49 CZ PHE A 6 0.960 5.159 5.051 1.00 4.45 C ATOM 50 OXT PHE A 6 0.375 0.720 10.569 1.00 8.77 O TER 51 PHE A 6 HETATM 52 O HOH A 11 2.789 2.185 11.242 1.00 9.88 O HETATM 53 O HOH A 12 -0.596 4.508 -7.919 1.00 20.08 O HETATM 54 O HOH A 13 1.919 3.469 -9.338 1.00 22.20 O HETATM 55 O HOH A 14 2.040 5.940 -8.264 1.00 29.38 O MASTER 241 0 0 0 0 0 0 6 54 1 0 1 END