PDB Short entry for 2OMQ HEADER PROTEIN FIBRIL 22-JAN-07 2OMQ TITLE VEALYL PEPTIDE DERIVED FROM HUMAN INSULIN CHAIN B, RESIDUES 12-17 COMPND MOL_ID: 1; COMPND 2 MOLECULE: VEALYL PEPTIDE DERIVED FROM HUMAN INSULIN CHAIN B, RESIDUES COMPND 3 12-17; COMPND 4 CHAIN: A, B, C, D; COMPND 5 FRAGMENT: RESIDUES 12-17; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS STERIC ZIPPER, ANTI-PARALLEL BETA-SHEET, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR M.IVANOVA,M.R.SAWAYA,D.EISENBERG REVDAT 6 18-OCT-17 2OMQ 1 REMARK REVDAT 5 22-APR-15 2OMQ 1 TITLE COMPND REVDAT 4 25-JUN-14 2OMQ 1 REMARK VERSN REVDAT 3 24-FEB-09 2OMQ 1 VERSN REVDAT 2 05-JUN-07 2OMQ 1 JRNL REVDAT 1 30-JAN-07 2OMQ 0 JRNL AUTH M.R.SAWAYA,S.SAMBASHIVAN,R.NELSON,M.I.IVANOVA,S.A.SIEVERS, JRNL AUTH 2 M.I.APOSTOL,M.J.THOMPSON,M.BALBIRNIE,J.J.WILTZIUS, JRNL AUTH 3 H.T.MCFARLANE,A.MADSEN,C.RIEKEL,D.EISENBERG JRNL TITL ATOMIC STRUCTURES OF AMYLOID CROSS-BETA SPINES REVEAL VARIED JRNL TITL 2 STERIC ZIPPERS. JRNL REF NATURE V. 447 453 2007 JRNL REFN ISSN 0028-0836 JRNL PMID 17468747 JRNL DOI 10.1038/NATURE05695 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 83.3 REMARK 3 NUMBER OF REFLECTIONS : 820 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) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 40 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 49 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.48 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 200 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) : 17.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.14000 REMARK 3 B22 (A**2) : 0.34000 REMARK 3 B33 (A**2) : -2.12000 REMARK 3 B12 (A**2) : 0.41000 REMARK 3 B13 (A**2) : 0.99000 REMARK 3 B23 (A**2) : -0.09000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.293 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.192 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.375 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.913 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 200 ; 0.009 ; 0.023 REMARK 3 BOND LENGTHS OTHERS (A): 208 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 272 ; 2.271 ; 2.106 REMARK 3 BOND ANGLES OTHERS (DEGREES): 472 ; 3.119 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 20 ; 7.878 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 8 ;33.309 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 32 ;13.076 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 36 ; 0.036 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 204 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 36 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 28 ; 0.224 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 159 ; 0.253 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 81 ; 0.214 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 103 ; 0.136 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 5 ; 0.287 ; 0.200 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): 11 ; 0.204 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 59 ; 0.227 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.192 ; 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): 120 ; 5.574 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 56 ; 0.000 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 188 ; 6.952 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 80 ; 7.371 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 84 ;10.186 ; 4.500 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 : 1.20 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 2OMQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JAN-07. REMARK 100 THE DEPOSITION ID IS D_1000041327. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUL-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 2.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.94660 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 820 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 90.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.17200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 3.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.41300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: POLYALANINE BETA STRANDS WITH IDEAL GEOMETRY 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: 2MM PEPTIDE IN 100 MM NACL AND 50 MM REMARK 280 PHOSPHATE. CRYSTALS CAN BE MORE EASILY REPRODUCED BY DISSOLVING REMARK 280 PEPTIDE TO 2 MM IN WATER AT ROOM TEMPERATURE, PH 2.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 310K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 300 REMARK: A STERIC ZIPPER CAN BE GENERATED BY REPEATED UNIT CELL REMARK 300 TRANSLATIONS OF THE ASYMMETRIC UNIT ALONG THE B AXIS. 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: OCTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 -1.82272 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 9.43862 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 DBREF 2OMQ A 1 6 PDB 2OMQ 2OMQ 1 6 DBREF 2OMQ B 1 6 PDB 2OMQ 2OMQ 1 6 DBREF 2OMQ C 1 6 PDB 2OMQ 2OMQ 1 6 DBREF 2OMQ D 1 6 PDB 2OMQ 2OMQ 1 6 SEQRES 1 A 6 VAL GLU ALA LEU TYR LEU SEQRES 1 B 6 VAL GLU ALA LEU TYR LEU SEQRES 1 C 6 VAL GLU ALA LEU TYR LEU SEQRES 1 D 6 VAL GLU ALA LEU TYR LEU FORMUL 5 HOH *4(H2 O) SHEET 1 A 2 GLU A 2 TYR A 5 0 SHEET 2 A 2 GLU B 2 TYR B 5 -1 O ALA B 3 N LEU A 4 SHEET 1 B 2 GLU C 2 TYR C 5 0 SHEET 2 B 2 GLU D 2 TYR D 5 -1 O TYR D 5 N GLU C 2 CRYST1 18.425 9.613 21.975 90.88 96.12 100.93 P 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 0.054274 0.010485 0.006203 0.00000 SCALE2 0.000000 0.105949 0.003856 0.00000 SCALE3 0.000000 0.000000 0.045797 0.00000