PDB Short entry for 2ONX HEADER PROTEIN FIBRIL 24-JAN-07 2ONX TITLE NNQQ PEPTIDE CORRESPONDING TO RESIDUES 8-11 OF YEAST PRION SUP35 TITLE 2 (ALTERNATE CRYSTAL FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE CORRESPONDING TO RESIDUES 8-11 OF YEAST PRION COMPND 3 SUP35; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: RESIDUES 8-11; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS STERIC ZIPPER, BETA SHEETS, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR M.R.SAWAYA,S.SAMBASHIVAN,R.NELSON,M.IVANOVA,S.A.SIEVERS,M.I.APOSTOL, AUTHOR 2 M.J.THOMPSON,M.BALBIRNIE,J.J.WILTZIUS,H.MCFARLANE,A.O.MADSEN, AUTHOR 3 C.RIEKEL,D.EISENBERG REVDAT 5 30-AUG-23 2ONX 1 REMARK REVDAT 4 18-OCT-17 2ONX 1 REMARK REVDAT 3 24-FEB-09 2ONX 1 VERSN REVDAT 2 05-JUN-07 2ONX 1 JRNL REVDAT 1 06-FEB-07 2ONX 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. 1.52 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) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.43 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 66.1 REMARK 3 NUMBER OF REFLECTIONS : 251 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 11.200 REMARK 3 FREE R VALUE TEST SET COUNT : 28 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) : 1.52 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 9 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 33.33 REMARK 3 BIN R VALUE (WORKING SET) : 0.5560 REMARK 3 BIN FREE R VALUE SET COUNT : 2 REMARK 3 BIN FREE R VALUE : 0.4870 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 35 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.65000 REMARK 3 B22 (A**2) : 0.16000 REMARK 3 B33 (A**2) : 1.59000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.39000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.203 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.146 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.072 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.275 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 34 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 19 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 45 ; 1.314 ; 1.851 REMARK 3 BOND ANGLES OTHERS (DEGREES): 48 ; 0.926 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 3 ; 6.443 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 4 ;49.819 ;30.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 6 ;12.152 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 4 ; 0.148 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 41 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 3 ; 0.000 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1 ; 0.201 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 16 ; 0.165 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 12 ; 0.158 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 21 ; 0.066 ; 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): 9 ; 0.178 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.170 ; 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): 26 ; 4.914 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 7 ; 1.240 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 31 ; 8.154 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 16 ; 5.002 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 14 ; 7.297 ; 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 2ONX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JAN-07. REMARK 100 THE DEPOSITION ID IS D_1000041369. 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 : 5.6 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 : 259 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 63.8 REMARK 200 DATA REDUNDANCY : 1.500 REMARK 200 R MERGE (I) : 0.15200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.1000 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 (%) : 26.1 REMARK 200 DATA REDUNDANCY IN SHELL : 1.20 REMARK 200 R MERGE FOR SHELL (I) : 0.29900 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: PDB ENTRY 1YJP 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: 30-50 MG/ML PEPTIDE DISOLVED IN WATER REMARK 280 AND MIXED WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION CONSISTING REMARK 280 OF 100 MM TRISODIUM CITRATE, 20% POLYETHYLENE GLYCOL 4000 AND 20% REMARK 280 ISOPROPANOL, PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 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 8.00700 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" UNIT CELL DIMENSION. THE SECOND SHEET OF THE STERIC ZIPPER CAN REMARK 300 BE GENERATED BY APPLICATION OF THE CRYSTALLOGRAPHIC OPERATOR -X,1/2+ REMARK 300 Y,1-Z, AND REPEATED UNIT CELL TRANSLATIONS OF THIS STRAND ALONG THE REMARK 300 "A" UNIT CELL DIMENSION. 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 4.85400 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 -1.87034 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 8.00700 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 15.43308 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 2.98366 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 8.00700 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 15.43308 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YJP RELATED DB: PDB REMARK 900 RELATED ID: 1YJO RELATED DB: PDB REMARK 900 RELATED ID: 2OKZ RELATED DB: PDB REMARK 900 RELATED ID: 2OLX RELATED DB: PDB DBREF 2ONX A 1 4 PDB 2ONX 2ONX 1 4 SEQRES 1 A 4 ASN ASN GLN GLN CRYST1 4.854 16.014 15.546 90.00 96.91 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 0.206016 0.000000 0.024967 0.00000 SCALE2 0.000000 0.062445 0.000000 0.00000 SCALE3 0.000000 0.000000 0.064796 0.00000