PDB Short entry for 2ONV
HEADER    PROTEIN FIBRIL                          24-JAN-07   2ONV              
TITLE     CRYSTAL STRUCTURE OF THE AMYLOID-FIBRIL FORMING PEPTIDE GGVVIA DERIVED
TITLE    2 FROM THE ALZHEIMER'S AMYLOID ABETA (ABETA37-42).                     
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: AMYLOID-FIBRIL FORMING PEPTIDE GGVVIA DERIVED FROM THE     
COMPND   3 ALZHEIMER'S AMYLOID ABETA;                                           
COMPND   4 CHAIN: A;                                                            
COMPND   5 FRAGMENT: RESIDUES 37-42;                                            
COMPND   6 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 SYNTHETIC: YES;                                                      
SOURCE   3 OTHER_DETAILS: PEPTIDE WAS COMMERCIALLY SYNTHESIZED BY CSBIO.        
KEYWDS    STERIC ZIPPER, BETA SHEETS, PROTEIN FIBRIL                            
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    S.SAMBASHIVAN,M.R.SAWAYA,D.EISENBERG                                  
REVDAT   4   18-OCT-17 2ONV    1       REMARK                                   
REVDAT   3   24-FEB-09 2ONV    1       VERSN                                    
REVDAT   2   05-JUN-07 2ONV    1       JRNL                                     
REVDAT   1   06-FEB-07 2ONV    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.    1.61 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) : 1.61                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 20.57                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 96.4                           
REMARK   3   NUMBER OF REFLECTIONS             : 515                            
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) : 0.235                           
REMARK   3   R VALUE            (WORKING SET) : 0.228                           
REMARK   3   FREE R VALUE                     : 0.299                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 9.900                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 51                              
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) : 1.61                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 1.65                         
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 22                           
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 88.46                        
REMARK   3   BIN R VALUE           (WORKING SET) : 0.3240                       
REMARK   3   BIN FREE R VALUE SET COUNT          : 1                            
REMARK   3   BIN FREE R VALUE                    : 0.0070                       
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 36                                      
REMARK   3   NUCLEIC ACID ATOMS       : 0                                       
REMARK   3   HETEROGEN ATOMS          : 0                                       
REMARK   3   SOLVENT ATOMS            : 3                                       
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 15.96                          
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 9.99                           
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : 0.70000                                              
REMARK   3    B22 (A**2) : 0.89000                                              
REMARK   3    B33 (A**2) : -1.59000                                             
REMARK   3    B12 (A**2) : 0.00000                                              
REMARK   3    B13 (A**2) : 0.00000                                              
REMARK   3    B23 (A**2) : 0.00000                                              
REMARK   3                                                                      
REMARK   3  ESTIMATED OVERALL COORDINATE ERROR.                                 
REMARK   3   ESU BASED ON R VALUE                            (A): 0.137         
REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.146         
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.136         
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.479         
REMARK   3                                                                      
REMARK   3 CORRELATION COEFFICIENTS.                                            
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.957                         
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.852                         
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT      
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):    35 ; 0.012 ; 0.023       
REMARK   3   BOND LENGTHS OTHERS               (A):    18 ; 0.002 ; 0.020       
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):    47 ; 1.859 ; 2.040       
REMARK   3   BOND ANGLES OTHERS          (DEGREES):    46 ; 1.041 ; 3.000       
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):     5 ; 8.031 ; 5.000       
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):  NULL ;  NULL ;  NULL       
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):     4 ; 1.738 ;15.000       
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):  NULL ;  NULL ;  NULL       
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):     7 ; 0.084 ; 0.200       
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):    39 ; 0.004 ; 0.020       
REMARK   3   GENERAL PLANES OTHERS             (A):     5 ; 0.000 ; 0.020       
REMARK   3   NON-BONDED CONTACTS REFINED ATOMS (A):     1 ; 0.026 ; 0.200       
REMARK   3   NON-BONDED CONTACTS OTHERS        (A):    12 ; 0.182 ; 0.200       
REMARK   3   NON-BONDED TORSION REFINED ATOMS  (A):    17 ; 0.158 ; 0.200       
REMARK   3   NON-BONDED TORSION OTHERS         (A):    19 ; 0.078 ; 0.200       
REMARK   3   H-BOND (X...Y) REFINED ATOMS      (A):     2 ; 0.352 ; 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):     4 ; 0.160 ; 0.200       
REMARK   3   SYMMETRY VDW OTHERS               (A):     8 ; 0.273 ; 0.200       
REMARK   3   SYMMETRY H-BOND REFINED ATOMS     (A):     3 ; 0.148 ; 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):    35 ; 1.388 ; 1.500       
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):    13 ; 0.137 ; 1.500       
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):    43 ; 1.773 ; 2.000       
REMARK   3   MAIN-CHAIN ANGLE OTHER ATOMS   (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):     7 ; 0.651 ; 3.000       
REMARK   3   SIDE-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):     4 ; 0.890 ; 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   : 1.40                                          
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 2ONV 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_1000041367.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 17-DEC-05                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : NULL                               
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   : 532                                
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.600                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 90.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 96.7                               
REMARK 200  DATA REDUNDANCY                : 4.500                              
REMARK 200  R MERGE                    (I) : 0.19200                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 12.6000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.72                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 96.7                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 4.90                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.42000                            
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: EXTENDED BETA STRAND GGVVIA                          
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 23.31                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.60                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: PEPTIDE CONCENTRATION: 15.0 MG/ML,       
REMARK 280  PEPTIDE:RESERVOIR:ADDITIVE RATIO 5:4:1, RESERVOIR: 2.0M AMMONIUM    
REMARK 280  SULFATE, ADDITIVE: 3.0% 0.1M HEXAMINE COBALT (III) CHLORIDE ,       
REMARK 280  VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K                     
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2                        
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X,-Y,Z                                                 
REMARK 290       3555   -X+1/2,Y+1/2,-Z                                         
REMARK 290       4555   X+1/2,-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        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        8.38000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       20.56700            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000        0.00000            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000        8.38000            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       20.56700            
REMARK 290   SMTRY3   4  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 BIOLOGICAL UNIT IS A PAIR OF SHEETS. BETA STRANDS        
REMARK 300 WITHIN THE SHEET ARE GENERATED BY UNIT CELL TRANSLATIONS ALONG THE   
REMARK 300 Z-AXIS. THE SECOND SHEET IN THE PAIR OF SHEETS IS GENERATED BY       
REMARK 300 APPLYING THE SYMMETRY OPERATOR X+1/2, -Y+1/2, -Z. WITHIN THE SECOND  
REMARK 300 SHEET ALSO, BETA STRANDS ARE GENERATED BY UNIT CELL TRANSLATIONS     
REMARK 300 ALONG THE Z-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: 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        0.00000            
REMARK 350   BIOMT2   2  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   2  0.000000  0.000000  1.000000        4.78900            
REMARK 350   BIOMT1   3  1.000000  0.000000  0.000000        8.38000            
REMARK 350   BIOMT2   3  0.000000 -1.000000  0.000000       20.56700            
REMARK 350   BIOMT3   3  0.000000  0.000000 -1.000000        0.00000            
REMARK 350   BIOMT1   4  1.000000  0.000000  0.000000        8.38000            
REMARK 350   BIOMT2   4  0.000000 -1.000000  0.000000       20.56700            
REMARK 350   BIOMT3   4  0.000000  0.000000 -1.000000        4.78900            
DBREF  2ONV A    1     6  PDB    2ONV     2ONV             1      6             
SEQRES   1 A    6  GLY GLY VAL VAL ILE ALA                                      
FORMUL   2  HOH   *3(H2 O)                                                      
CRYST1   16.760   41.134    4.789  90.00  90.00  90.00 P 21 21 2     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      0.059666  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.024311  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.208812        0.00000