PDB Short entry for 1H95
HEADER    TRANSLATION FACTOR                      23-FEB-01   1H95              
TITLE     SOLUTION STRUCTURE OF THE SINGLE-STRANDED DNA-BINDING COLD            
TITLE    2 SHOCK DOMAIN (CSD) OF HUMAN Y-BOX PROTEIN 1 (YB1)                    
TITLE    3 DETERMINED BY NMR (10 LOWEST ENERGY STRUCTURES)                      
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: Y-BOX BINDING PROTEIN;                                     
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: COLD SHOCK DOMAIN;                                         
COMPND   5 SYNONYM: CSD;                                                        
COMPND   6 ENGINEERED: YES;                                                     
COMPND   7 OTHER_DETAILS: SINGLE STRANDED DNA BINDING COLD SHOCK                
COMPND   8  DOMAIN(CSD) OF HUMAN Y-BOX PROTEIN 1 (YB-1)                         
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE   3 ORGANISM_COMMON: HUMAN;                                              
SOURCE   4 ORGANISM_TAXID: 9606;                                                
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 469008;                                     
SOURCE   7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);                                 
SOURCE   8 EXPRESSION_SYSTEM_PLASMID: PET11A                                    
KEYWDS    TRANSLATION FACTOR, TRANSCRIPTION FACTOR, OB-FOLD, 5-                 
KEYWDS   2 STRANDED ANTI-PARALLEL BETA-BARREL, SINGLE STRANDED DNA              
KEYWDS   3 BINDING, COLD SHOCK, Y-BOX                                           
EXPDTA    SOLUTION NMR                                                          
NUMMDL    10                                                                    
AUTHOR    C.P.A.M.KLOKS,C.A.E.M.SPRONK,A.HOFFMANN,G.W.VUISTER,                  
AUTHOR   2 S.GRZESIEK,C.W.HILBERS                                               
REVDAT   2   24-FEB-09 1H95    1       VERSN                                    
REVDAT   1   21-FEB-02 1H95    0                                                
JRNL        AUTH   C.P.A.M.KLOKS,C.A.E.M.SPRONK,E.LASONDER,A.HOFFMANN,          
JRNL        AUTH 2 G.W.VUISTER,S.GRZESIEK,C.W.HILBERS                           
JRNL        TITL   THE SOLUTION STRUCTURE AND DNA-BINDING PROPERTIES            
JRNL        TITL 2 OF THE COLD-SHOCK DOMAIN OF THE HUMAN Y-BOX                  
JRNL        TITL 3 PROTEIN YB-1.                                                
JRNL        REF    J.MOL.BIOL.                   V. 316   317 2002              
JRNL        REFN                   ISSN 0022-2836                               
JRNL        PMID   11851341                                                     
JRNL        DOI    10.1006/JMBI.2001.5334                                       
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : MICHEAL NILGES X-PLOR X-PLOR                         
REMARK   3   AUTHORS     : NILGES                                               
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: RESTRAINED MD                             
REMARK   4                                                                      
REMARK   4 1H95 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-FEB-01.                  
REMARK 100 THE PDBE ID CODE IS EBI-5936.                                        
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 303                                
REMARK 210  PH                             : 6.7                                
REMARK 210  IONIC STRENGTH                 : 0                                  
REMARK 210  PRESSURE                       : 1 ATM                              
REMARK 210  SAMPLE CONTENTS                : NULL                               
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 15N-EDITED NOESY,                  
REMARK 210                                   15N-EDITED ROESY,                  
REMARK 210                                   13C-EDITED NOESY, HNHA             
REMARK 210  SPECTROMETER FIELD STRENGTH    : 500; 600; 750                      
REMARK 210  SPECTROMETER MODEL             : INOVA500; INOVA750;                
REMARK 210                                   DRX600                             
REMARK 210  SPECTROMETER MANUFACTURER      : VARIAN; VARIAN; BRUKER             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : NMRPIPE, PIPP, X-PLOR              
REMARK 210   METHOD USED                   : TORSION ANGLE DYNAMICS             
REMARK 210                                   FOLLOWED BY RESTRAINED MD          
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 10                                 
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 10                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : NULL                               
REMARK 210                                                                      
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1                   
REMARK 210                                                                      
REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE          
REMARK 210 NMR SPECTROSCOPY ON 15N AND 15N/13C LABELLED COLD SHOCK              
REMARK 210 DOMAIN OF HUMAN YB-1                                                 
REMARK 215                                                                      
REMARK 215 NMR STUDY                                                            
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION           
REMARK 215 NMR DATA.  PROTEIN DATA BANK CONVENTIONS REQUIRE THAT                
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON              
REMARK 215 THESE RECORDS ARE MEANINGLESS.                                       
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES                                       
REMARK 500                                                                      
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES              
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE               
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                 
REMARK 500                                                                      
REMARK 500 STANDARD TABLE:                                                      
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)              
REMARK 500                                                                      
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999                        
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996                     
REMARK 500                                                                      
REMARK 500  M RES CSSEQI ATM1   ATM2   ATM3                                     
REMARK 500  1 ARG A  27   NE  -  CZ  -  NH1 ANGL. DEV. =   3.5 DEGREES          
REMARK 500  2 ARG A  51   NE  -  CZ  -  NH1 ANGL. DEV. =   3.3 DEGREES          
REMARK 500  3 ARG A  19   NE  -  CZ  -  NH1 ANGL. DEV. =   3.6 DEGREES          
REMARK 500  3 ARG A  27   NE  -  CZ  -  NH1 ANGL. DEV. =   4.2 DEGREES          
REMARK 500  7 ARG A  19   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.1 DEGREES          
REMARK 500  7 ARG A  51   NE  -  CZ  -  NH1 ANGL. DEV. =   3.0 DEGREES          
REMARK 500  8 ARG A  27   NE  -  CZ  -  NH1 ANGL. DEV. =   3.1 DEGREES          
REMARK 500  8 ARG A  47   NE  -  CZ  -  NH1 ANGL. DEV. =   3.3 DEGREES          
REMARK 500  8 ARG A  51   NE  -  CZ  -  NH1 ANGL. DEV. =   3.4 DEGREES          
REMARK 500  9 ARG A  47   NE  -  CZ  -  NH1 ANGL. DEV. =   3.2 DEGREES          
REMARK 500 10 ARG A  47   NE  -  CZ  -  NH1 ANGL. DEV. =   3.3 DEGREES          
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: TORSION ANGLES                                             
REMARK 500                                                                      
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:            
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                             
REMARK 500 STANDARD TABLE:                                                      
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)                    
REMARK 500                                                                      
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-           
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400            
REMARK 500                                                                      
REMARK 500  M RES CSSEQI        PSI       PHI                                   
REMARK 500  1 LYS A   3      -98.61   -116.64                                   
REMARK 500  1 ILE A   5      -61.49    -91.37                                   
REMARK 500  1 TRP A  15       63.67     37.11                                   
REMARK 500  1 LYS A  43     -118.54     56.75                                   
REMARK 500  1 ARG A  47       60.07   -112.19                                   
REMARK 500  1 TYR A  49      144.38     70.77                                   
REMARK 500  1 LEU A  50      -81.30    -93.29                                   
REMARK 500  1 GLU A  67      -71.23   -100.35                                   
REMARK 500  1 GLU A  71     -162.86   -122.37                                   
REMARK 500  2 ILE A   5      -72.87    -95.61                                   
REMARK 500  2 LYS A  14      -87.29   -100.32                                   
REMARK 500  2 LYS A  42     -172.53     65.34                                   
REMARK 500  2 ASN A  44      -86.98     53.21                                   
REMARK 500  2 LYS A  48     -157.44     66.74                                   
REMARK 500  2 GLU A  67     -136.61    -95.37                                   
REMARK 500  2 GLU A  71     -166.71   -107.01                                   
REMARK 500  3 LYS A   2      -76.52    -90.58                                   
REMARK 500  3 VAL A   4       86.76     70.73                                   
REMARK 500  3 ILE A   5      -72.08    -80.74                                   
REMARK 500  3 LYS A   8       75.67     59.18                                   
REMARK 500  3 ASN A  17       76.90   -102.52                                   
REMARK 500  3 ASN A  28       84.95    -62.48                                   
REMARK 500  3 ASP A  29      -76.12   -159.42                                   
REMARK 500  3 LYS A  31       81.76     55.65                                   
REMARK 500  3 LYS A  48     -156.52     59.32                                   
REMARK 500  3 LEU A  50     -143.21    -88.32                                   
REMARK 500  3 GLU A  67     -145.37    -78.30                                   
REMARK 500  3 GLU A  71     -168.10   -121.09                                   
REMARK 500  3 ASN A  74       63.36     34.51                                   
REMARK 500  4 LYS A   8       83.01     53.38                                   
REMARK 500  4 THR A  30       33.89   -143.22                                   
REMARK 500  4 TYR A  49     -147.64    -86.81                                   
REMARK 500  4 ARG A  51      -83.21   -139.71                                   
REMARK 500  4 GLU A  67      -89.57   -107.82                                   
REMARK 500  5 LYS A   3      -98.90     75.38                                   
REMARK 500  5 ASP A  29      -81.33    -76.25                                   
REMARK 500  5 LYS A  31       62.29     77.57                                   
REMARK 500  5 ASN A  44      -80.39    -76.73                                   
REMARK 500  5 TYR A  49      159.74     66.32                                   
REMARK 500  5 GLU A  67      -69.78   -101.75                                   
REMARK 500  6 LYS A   8       73.15     60.95                                   
REMARK 500  6 LYS A  14      -86.95   -105.37                                   
REMARK 500  6 ASN A  28       48.00    -82.54                                   
REMARK 500  6 THR A  30       35.33   -150.34                                   
REMARK 500  6 LYS A  31       75.99     57.87                                   
REMARK 500  6 LYS A  42      -74.91    -73.43                                   
REMARK 500  6 TYR A  49       56.82    -97.93                                   
REMARK 500  6 ARG A  51       79.79   -101.49                                   
REMARK 500  6 SER A  52      -85.58   -107.02                                   
REMARK 500  6 GLU A  67     -145.47   -123.67                                   
REMARK 500  6 GLU A  71     -168.04   -120.53                                   
REMARK 500  7 LYS A   2      -72.20     60.83                                   
REMARK 500  7 LYS A   3       88.27     76.79                                   
REMARK 500  7 VAL A   4      -72.54   -113.97                                   
REMARK 500  7 TRP A  15      154.11     77.83                                   
REMARK 500  7 ASP A  29      -76.56   -166.97                                   
REMARK 500  7 LYS A  31       73.39     51.12                                   
REMARK 500  7 ASN A  44      -49.13     69.53                                   
REMARK 500  7 LEU A  50      -86.83    -82.16                                   
REMARK 500  8 LYS A   3      103.29    -48.45                                   
REMARK 500  8 VAL A   4      103.64     61.90                                   
REMARK 500  8 TRP A  15      -79.29    -69.83                                   
REMARK 500  8 PHE A  16      114.69     75.10                                   
REMARK 500  8 THR A  30       24.59   -146.40                                   
REMARK 500  8 LYS A  31       76.37     67.09                                   
REMARK 500  8 TYR A  49      166.81     75.85                                   
REMARK 500  8 ARG A  51      112.76     71.41                                   
REMARK 500  8 SER A  52      -70.37    -81.23                                   
REMARK 500  9 LYS A   3      -97.16    -79.14                                   
REMARK 500  9 VAL A   4      117.15     65.61                                   
REMARK 500  9 LYS A  14      -99.14   -102.47                                   
REMARK 500  9 ARG A  27      147.65    -36.12                                   
REMARK 500  9 ASP A  29      -78.51    -82.94                                   
REMARK 500  9 LYS A  31       67.53     60.09                                   
REMARK 500  9 ASN A  45       68.58   -118.53                                   
REMARK 500  9 LYS A  48      -93.38    -92.50                                   
REMARK 500  9 LEU A  50      -60.51     74.20                                   
REMARK 500  9 GLU A  67     -136.23    -89.45                                   
REMARK 500 10 LYS A   3      -28.65   -145.78                                   
REMARK 500 10 LYS A   8       73.12     59.05                                   
REMARK 500 10 LYS A  14     -100.69    -95.14                                   
REMARK 500 10 ASP A  29      -72.57   -132.42                                   
REMARK 500 10 ARG A  47      -81.25   -107.54                                   
REMARK 500 10 GLU A  67      -85.26    -80.12                                   
REMARK 500 10 GLU A  71     -166.81   -117.83                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: PLANAR GROUPS                                              
REMARK 500                                                                      
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL                 
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE                    
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN                    
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS                        
REMARK 500 AN RMSD GREATER THAN THIS VALUE                                      
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                             
REMARK 500                                                                      
REMARK 500  M RES CSSEQI        RMS     TYPE                                    
REMARK 500  3 ARG A  27         0.11    SIDE CHAIN                              
REMARK 500  4 ARG A  27         0.11    SIDE CHAIN                              
REMARK 500  4 ARG A  51         0.08    SIDE CHAIN                              
REMARK 500  6 ARG A  27         0.08    SIDE CHAIN                              
REMARK 500  7 ARG A  27         0.12    SIDE CHAIN                              
REMARK 500 10 ARG A  19         0.09    SIDE CHAIN                              
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: CHIRAL CENTERS                                             
REMARK 500                                                                      
REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL                     
REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY                      
REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN                            
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE                   
REMARK 500                                                                      
REMARK 500 STANDARD TABLE:                                                      
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16)       
REMARK 500                                                                      
REMARK 500  M RES CSSEQI    IMPROPER   EXPECTED   FOUND DETAILS                 
REMARK 500  1 ASN A  28        23.1      L          L   OUTSIDE RANGE           
REMARK 500  3 ASN A  74        24.2      L          L   OUTSIDE RANGE           
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 700                                                                      
REMARK 700 SHEET                                                                
REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED.                               
REMARK 999                                                                      
REMARK 999 SEQUENCE                                                             
REMARK 999 THE SEQUENCE IS MATCHES TO SWISS PROT ENTRY Q90376 (RESIDUES         
REMARK 999 15-92) WHICH REPRESENTS Y-BOX BINDING PROTEIN FROM COLUMBA LIVIA     
REMARK 999 (DOMESTIC PIGEON).                                                   
REMARK 999 N-TERMINAL METHIONINE ADDED IN PDB-SEQUENCE                          
DBREF  1H95 A    1    79  PDB    1H95     1H95             1     79             
SEQRES   1 A   79  MET LYS LYS VAL ILE ALA THR LYS VAL LEU GLY THR VAL          
SEQRES   2 A   79  LYS TRP PHE ASN VAL ARG ASN GLY TYR GLY PHE ILE ASN          
SEQRES   3 A   79  ARG ASN ASP THR LYS GLU ASP VAL PHE VAL HIS GLN THR          
SEQRES   4 A   79  ALA ILE LYS LYS ASN ASN PRO ARG LYS TYR LEU ARG SER          
SEQRES   5 A   79  VAL GLY ASP GLY GLU THR VAL GLU PHE ASP VAL VAL GLU          
SEQRES   6 A   79  GLY GLU LYS GLY ALA GLU ALA ALA ASN VAL THR GLY PRO          
SEQRES   7 A   79  GLY                                                          
SHEET    1  AA 6 LYS A   3  VAL A  18  0                                        
SHEET    2  AA 6 GLU A  57  GLU A  65 -1  O  VAL A  59   N  GLY A  11           
SHEET    3  AA 6 GLY A  69  THR A  76 -1  O  GLU A  71   N  VAL A  64           
SHEET    4  AA 6 LYS A  31  HIS A  37  1  O  ASP A  33   N  ALA A  70           
SHEET    5  AA 6 GLY A  21  ASN A  28 -1  O  GLY A  23   N  VAL A  36           
SHEET    6  AA 6 LYS A   3  VAL A  18 -1  O  THR A  12   N  ASN A  26           
CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1          
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      1.000000  0.000000  0.000000        0.00000                         
SCALE2      0.000000  1.000000  0.000000        0.00000                         
SCALE3      0.000000  0.000000  1.000000        0.00000