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 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 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
ATOM 1 N ASN A 1 0.452 2.495 0.430 1.00 13.01 N
ATOM 2 CA ASN A 1 0.395 3.556 1.478 1.00 15.49 C
ATOM 3 C ASN A 1 -0.265 3.026 2.741 1.00 17.59 C
ATOM 4 O ASN A 1 -1.491 3.018 2.841 1.00 22.47 O
ATOM 5 CB ASN A 1 -0.357 4.785 0.989 1.00 23.58 C
ATOM 6 CG ASN A 1 0.413 5.575 -0.038 1.00 33.44 C
ATOM 7 OD1 ASN A 1 1.123 6.520 0.300 1.00 40.45 O
ATOM 8 ND2 ASN A 1 0.280 5.193 -1.305 1.00 32.63 N
ATOM 9 N ASN A 2 0.558 2.552 3.675 1.00 8.09 N
ATOM 10 CA ASN A 2 0.140 2.007 4.983 1.00 7.76 C
ATOM 11 C ASN A 2 0.620 2.936 6.093 1.00 10.30 C
ATOM 12 O ASN A 2 1.782 3.318 6.098 1.00 13.35 O
ATOM 13 CB ASN A 2 0.827 0.661 5.208 1.00 5.39 C
ATOM 14 CG ASN A 2 0.222 -0.450 4.441 1.00 11.18 C
ATOM 15 OD1 ASN A 2 -0.957 -0.425 4.134 1.00 14.38 O
ATOM 16 ND2 ASN A 2 1.007 -1.500 4.203 1.00 11.50 N
ATOM 17 N GLN A 3 -0.251 3.283 7.036 1.00 9.07 N
ATOM 18 CA GLN A 3 0.168 4.035 8.225 1.00 6.77 C
ATOM 19 C GLN A 3 -0.483 3.441 9.469 1.00 7.12 C
ATOM 20 O GLN A 3 -1.715 3.312 9.528 1.00 7.25 O
ATOM 21 CB GLN A 3 -0.179 5.530 8.149 1.00 10.37 C
ATOM 22 CG GLN A 3 0.537 6.314 7.109 1.00 7.68 C
ATOM 23 CD GLN A 3 0.053 7.762 7.086 1.00 9.06 C
ATOM 24 OE1 GLN A 3 -1.169 8.035 7.199 1.00 10.09 O
ATOM 25 NE2 GLN A 3 0.997 8.690 6.976 1.00 6.75 N
ATOM 26 N GLN A 4 0.339 3.060 10.461 1.00 12.42 N
ATOM 27 CA GLN A 4 -0.182 2.636 11.781 1.00 16.85 C
ATOM 28 C GLN A 4 0.753 2.947 12.952 1.00 28.21 C
ATOM 29 O GLN A 4 1.615 3.841 12.868 1.00 34.15 O
ATOM 30 CB GLN A 4 -0.526 1.156 11.784 1.00 18.06 C
ATOM 31 CG GLN A 4 0.648 0.212 11.888 1.00 12.50 C
ATOM 32 CD GLN A 4 0.233 -1.201 11.608 1.00 16.78 C
ATOM 33 OE1 GLN A 4 -0.963 -1.494 11.482 1.00 19.98 O
ATOM 34 NE2 GLN A 4 1.209 -2.096 11.524 1.00 9.66 N
ATOM 35 OXT GLN A 4 0.645 2.343 14.027 1.00 29.30 O
TER 36 GLN A 4
MASTER 250 0 0 0 0 0 0 6 35 1 0 1
END