HEADER PROTEIN FIBRIL 22-JAN-07 2OMP TITLE LYQLEN PEPTIDE DERIVED FROM HUMAN INSULIN CHAIN A, RESIDUES 13-18 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYQLEN PEPTIDE DERIVED FROM HUMAN INSULIN CHAIN A, RESIDUES COMPND 3 13-18; COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: RESIDUES 13-18; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS STERIC ZIPPER, ANTIPARALLEL BETA-SHEET, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR M.I.IVANOVA,M.R.SAWAYA,D.EISENBERG REVDAT 7 03-APR-24 2OMP 1 REMARK REVDAT 6 27-DEC-23 2OMP 1 REMARK REVDAT 5 18-OCT-17 2OMP 1 REMARK REVDAT 4 13-JUL-11 2OMP 1 VERSN REVDAT 3 24-FEB-09 2OMP 1 VERSN REVDAT 2 05-JUN-07 2OMP 1 JRNL REVDAT 1 30-JAN-07 2OMP 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.O.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. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.24 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 3 NUMBER OF REFLECTIONS : 682 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.000 REMARK 3 FREE R VALUE TEST SET COUNT : 41 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 38 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.3110 REMARK 3 BIN FREE R VALUE SET COUNT : 4 REMARK 3 BIN FREE R VALUE : 0.2880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 110 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 6 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 15.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 5.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.39000 REMARK 3 B22 (A**2) : -0.06000 REMARK 3 B33 (A**2) : 0.38000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.29000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.320 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.196 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.118 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.051 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.810 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 113 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 103 ; 0.012 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 152 ; 1.357 ; 2.072 REMARK 3 BOND ANGLES OTHERS (DEGREES): 241 ; 2.015 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 10 ; 5.755 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 8 ;45.743 ;27.500 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 22 ;18.223 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 17 ; 0.041 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 118 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 18 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 11 ; 0.190 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 62 ; 0.201 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 35 ; 0.194 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 70 ; 0.090 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 1 ; 0.126 ; 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): 3 ; 0.264 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 19 ; 0.186 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.211 ; 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): 91 ; 3.237 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 28 ; 0.045 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 95 ; 2.389 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 69 ; 5.139 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 57 ; 5.465 ; 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 6 REMARK 3 ORIGIN FOR THE GROUP (A): 1.1396 1.9733 -0.9879 REMARK 3 T TENSOR REMARK 3 T11: 0.0054 T22: 0.0137 REMARK 3 T33: -0.0249 T12: 0.0084 REMARK 3 T13: -0.0163 T23: 0.0251 REMARK 3 L TENSOR REMARK 3 L11: 0.3619 L22: 7.0650 REMARK 3 L33: 3.6373 L12: 1.5235 REMARK 3 L13: -1.1132 L23: -5.0590 REMARK 3 S TENSOR REMARK 3 S11: -0.1074 S12: -0.0113 S13: -0.0316 REMARK 3 S21: -0.0229 S22: 0.1190 S23: 0.0018 REMARK 3 S31: -0.0840 S32: -0.0397 S33: -0.0116 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 6 REMARK 3 ORIGIN FOR THE GROUP (A): 6.1002 2.2679 -0.4459 REMARK 3 T TENSOR REMARK 3 T11: -0.0298 T22: 0.0019 REMARK 3 T33: 0.0036 T12: 0.0061 REMARK 3 T13: 0.0053 T23: 0.0174 REMARK 3 L TENSOR REMARK 3 L11: 0.6913 L22: 6.7672 REMARK 3 L33: 4.4172 L12: 2.1575 REMARK 3 L13: -1.7460 L23: -5.4338 REMARK 3 S TENSOR REMARK 3 S11: 0.0682 S12: -0.0160 S13: -0.0785 REMARK 3 S21: 0.0174 S22: 0.0825 S23: 0.1744 REMARK 3 S31: -0.0720 S32: -0.1234 S33: -0.1507 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 2OMP 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_1000041326. 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 : 752 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 91.0 REMARK 200 DATA REDUNDANCY : 2.100 REMARK 200 R MERGE (I) : 0.18600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.8000 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 (%) : 83.5 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.40200 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: IDEALIZED BETA STRANDS, POLYALANINE 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: 20MM PEPTIDE IN 100 MM NACL AND 50 MM REMARK 280 PHOSPHATE, PH 2.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 310K 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 14.00150 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 300 REMARK: ONE SHEET OF THE STERIC ZIPPER CAN BE GENERATED BY REPEATED REMARK 300 APPLICATION OF THE CRYSTALLOGRAPHIC UNIT CELL TRANSLATION ALONG THE REMARK 300 A AXIS. THE SECOND SHEET OF THE STERIC ZIPPER CAN BE GENERATED BY REMARK 300 APPLICATION OF THE CRYSTALLOGRAPHIC OPERATOR X,Y,Z+1, AND REPEATED REMARK 300 UNIT CELL TRANSLATIONS OF THIS STRAND ALONG THE A 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 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 9.66600 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 -1.88540 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 17.24323 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 7.78060 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 17.24323 DBREF 2OMP A 1 6 PDB 2OMP 2OMP 1 6 DBREF 2OMP B 1 6 PDB 2OMP 2OMP 1 6 SEQRES 1 A 6 LEU TYR GLN LEU GLU ASN SEQRES 1 B 6 LEU TYR GLN LEU GLU ASN FORMUL 3 HOH *6(H2 O) SHEET 1 A 2 TYR A 2 GLU A 5 0 SHEET 2 A 2 TYR B 2 GLU B 5 -1 O LEU B 4 N GLN A 3 CRYST1 9.666 28.003 17.346 90.00 96.24 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 0.103455 0.000000 0.011305 0.00000 SCALE2 0.000000 0.035710 0.000000 0.00000 SCALE3 0.000000 0.000000 0.057993 0.00000