PDB Short entry for 2ONA HEADER PROTEIN FIBRIL 23-JAN-07 2ONA TITLE MVGGVV PEPTIDE DERIVED FROM ALZHEIMER'S A-BETA, RESIDUES 35-40 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MVGGVV PEPTIDE DERIVED FROM ALZHEIMER'S A-BETA, RESIDUES COMPND 3 35-40; COMPND 4 CHAIN: A, B, C, D; COMPND 5 FRAGMENT: RESIDUES 35-40; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS STERIC ZIPPER, BETA SHEET, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR S.SAMBASHIVAN,M.R.SAWAYA,D.EISENBERG REVDAT 6 03-APR-24 2ONA 1 REMARK REVDAT 5 27-DEC-23 2ONA 1 REMARK REVDAT 4 18-OCT-17 2ONA 1 REMARK REVDAT 3 24-FEB-09 2ONA 1 VERSN REVDAT 2 05-JUN-07 2ONA 1 JRNL REVDAT 1 30-JAN-07 2ONA 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. 2.03 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) : 2.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 409 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) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.800 REMARK 3 FREE R VALUE TEST SET COUNT : 44 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) : 2.03 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 REFLECTION IN BIN (WORKING SET) : 24 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 37.31 REMARK 3 BIN R VALUE (WORKING SET) : 0.2080 REMARK 3 BIN FREE R VALUE SET COUNT : 1 REMARK 3 BIN FREE R VALUE : 0.4080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 152 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 6 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.10000 REMARK 3 B22 (A**2) : 0.10000 REMARK 3 B33 (A**2) : -0.08000 REMARK 3 B12 (A**2) : -0.28000 REMARK 3 B13 (A**2) : 0.26000 REMARK 3 B23 (A**2) : -0.07000 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): 0.481 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.118 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.305 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 148 ; 0.009 ; 0.023 REMARK 3 BOND LENGTHS OTHERS (A): 80 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 196 ; 1.254 ; 2.057 REMARK 3 BOND ANGLES OTHERS (DEGREES): 204 ; 0.669 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 20 ; 2.560 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 24 ;18.457 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 28 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 156 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 20 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 19 ; 0.159 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 62 ; 0.180 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 66 ; 0.140 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 99 ; 0.085 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 5 ; 0.145 ; 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): 12 ; 0.230 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 16 ; 0.177 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.096 ; 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): 137 ; 1.732 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 52 ; 0.456 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 176 ; 1.821 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 37 ; 2.080 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 20 ; 2.628 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B C D REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1 A 6 5 REMARK 3 1 B 1 B 6 5 REMARK 3 1 C 1 C 6 5 REMARK 3 1 D 1 D 6 5 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 33 ; 0.490 ; 0.500 REMARK 3 MEDIUM POSITIONAL 1 B (A): 33 ; 0.550 ; 0.500 REMARK 3 MEDIUM POSITIONAL 1 C (A): 33 ; 0.140 ; 0.500 REMARK 3 MEDIUM POSITIONAL 1 D (A): 33 ; 0.170 ; 0.500 REMARK 3 LOOSE POSITIONAL 1 A (A): 25 ; 0.800 ; 5.000 REMARK 3 LOOSE POSITIONAL 1 B (A): 25 ; 1.030 ; 5.000 REMARK 3 LOOSE POSITIONAL 1 C (A): 25 ; 0.600 ; 5.000 REMARK 3 LOOSE POSITIONAL 1 D (A): 25 ; 0.500 ; 5.000 REMARK 3 MEDIUM THERMAL 1 A (A**2): 33 ; 0.460 ; 2.000 REMARK 3 MEDIUM THERMAL 1 B (A**2): 33 ; 0.490 ; 2.000 REMARK 3 MEDIUM THERMAL 1 C (A**2): 33 ; 0.540 ; 2.000 REMARK 3 MEDIUM THERMAL 1 D (A**2): 33 ; 0.690 ; 2.000 REMARK 3 LOOSE THERMAL 1 A (A**2): 25 ; 1.570 ;10.000 REMARK 3 LOOSE THERMAL 1 B (A**2): 25 ; 1.410 ;10.000 REMARK 3 LOOSE THERMAL 1 C (A**2): 25 ; 1.030 ;10.000 REMARK 3 LOOSE THERMAL 1 D (A**2): 25 ; 2.090 ;10.000 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 2ONA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JAN-07. REMARK 100 THE DEPOSITION ID IS D_1000041347. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-DEC-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 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) : 0.9466 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 : 409 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 90.2 REMARK 200 DATA REDUNDANCY : 1.600 REMARK 200 R MERGE (I) : 0.16000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.2 REMARK 200 DATA REDUNDANCY IN SHELL : 1.60 REMARK 200 R MERGE FOR SHELL (I) : 0.22200 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 IDEALIZED BETA STRAND 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 MG/ML PEPTIDE IN WATER MIXED 1:1 REMARK 280 WITH RESERVOIR CONTAINING 0.02 M CACL2, 30% MPD, 0.1 M SODIUM REMARK 280 ACETATE, PH 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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: THE STERIC ZIPPER CAN BE GENERATED BY REPEATED APPLICATION REMARK 300 OF THE CRYSTALLOGRAPHIC UNIT CELL TRANSLATION 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 0.51944 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 9.68508 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2OKZ RELATED DB: PDB REMARK 900 SAME PEPTIDE SEQUENCE IN A DIFFERENT CRYSTAL PACKING DBREF 2ONA A 1 6 PDB 2ONA 2ONA 1 6 DBREF 2ONA B 1 6 PDB 2ONA 2ONA 1 6 DBREF 2ONA C 1 6 PDB 2ONA 2ONA 1 6 DBREF 2ONA D 1 6 PDB 2ONA 2ONA 1 6 SEQRES 1 A 6 MET VAL GLY GLY VAL VAL SEQRES 1 B 6 MET VAL GLY GLY VAL VAL SEQRES 1 C 6 MET VAL GLY GLY VAL VAL SEQRES 1 D 6 MET VAL GLY GLY VAL VAL FORMUL 5 HOH *6(H2 O) SHEET 1 A 2 VAL A 2 VAL A 5 0 SHEET 2 A 2 VAL B 2 VAL B 5 -1 O VAL B 2 N VAL A 5 SHEET 1 B 2 VAL C 2 VAL C 5 0 SHEET 2 B 2 VAL D 2 VAL D 5 -1 O GLY D 4 N GLY C 3 CRYST1 25.862 9.699 15.851 77.18 74.69 86.93 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 0.038667 -0.002074 -0.010382 0.00000 SCALE2 0.000000 0.103252 -0.022808 0.00000 SCALE3 0.000000 0.000000 0.066986 0.00000