PDB Short entry for 1MJM
HEADER    TRANSCRIPTION/DNA                       30-JAN-98   1MJM              
TITLE     METHIONINE APOREPRESSOR MUTANT (Q44K) COMPLEXED TO HALF OF THE        
TITLE    2 CONSENSUS OPERATOR SEQUENCE                                          
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: HALF CONSENSUS DNA OPERATOR DUPLEX;                        
COMPND   3 CHAIN: C, D;                                                         
COMPND   4 ENGINEERED: YES;                                                     
COMPND   5 MOL_ID: 2;                                                           
COMPND   6 MOLECULE: METHIONINE REPRESSOR;                                      
COMPND   7 CHAIN: A, B;                                                         
COMPND   8 ENGINEERED: YES;                                                     
COMPND   9 MUTATION: YES                                                        
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 SYNTHETIC: YES;                                                      
SOURCE   3 MOL_ID: 2;                                                           
SOURCE   4 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;                               
SOURCE   5 ORGANISM_TAXID: 562;                                                 
SOURCE   6 GENE: METJ;                                                          
SOURCE   7 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   8 EXPRESSION_SYSTEM_TAXID: 562                                         
KEYWDS    TRANSCRIPTION REGULATION, METJ, METHIONINE REPRESSOR, SHEET-HELIX-    
KEYWDS   2 HELIX, S-ADENOSYL METHIONINE, DNA, COMPLEX (TRANSCRIPTION            
KEYWDS   3 REGULATION-DNA), TRANSCRIPTION-DNA COMPLEX                           
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    C.W.GARVIE,S.E.V.PHILLIPS                                             
REVDAT   5   03-NOV-21 1MJM    1       SEQADV                                   
REVDAT   4   24-FEB-09 1MJM    1       VERSN                                    
REVDAT   3   01-APR-03 1MJM    1       JRNL                                     
REVDAT   2   16-AUG-01 1MJM    5                                                
REVDAT   1   02-AUG-99 1MJM    0                                                
JRNL        AUTH   C.W.GARVIE,S.E.PHILLIPS                                      
JRNL        TITL   DIRECT AND INDIRECT READOUT IN MUTANT MET REPRESSOR-OPERATOR 
JRNL        TITL 2 COMPLEXES.                                                   
JRNL        REF    STRUCTURE FOLD.DES.           V.   8   905 2000              
JRNL        REFN                   ISSN 0969-2126                               
JRNL        PMID   10986458                                                     
JRNL        DOI    10.1016/S0969-2126(00)00182-9                                
REMARK   2                                                                      
REMARK   2 RESOLUTION.    2.20 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : X-PLOR 3.860                                         
REMARK   3   AUTHORS     : BRUNGER                                              
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 25.40                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000                          
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : 10000000.000                   
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : 0.0010                         
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 88.6                           
REMARK   3   NUMBER OF REFLECTIONS             : 13755                          
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 SET) : 0.227                           
REMARK   3   FREE R VALUE                     : 0.282                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.300                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 725                             
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : 0.010                           
REMARK   3                                                                      
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.                                  
REMARK   3   TOTAL NUMBER OF BINS USED           : 15                           
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 2.20                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.25                         
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 53.70                        
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : 505                          
REMARK   3   BIN R VALUE           (WORKING SET) : 0.3630                       
REMARK   3   BIN FREE R VALUE                    : 0.3390                       
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : 3.20                         
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : 32                           
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : 0.063                        
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 1690                                    
REMARK   3   NUCLEIC ACID ATOMS       : 404                                     
REMARK   3   HETEROGEN ATOMS          : 0                                       
REMARK   3   SOLVENT ATOMS            : 177                                     
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 25.70                          
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 28.00                          
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : NULL                                                 
REMARK   3    B22 (A**2) : NULL                                                 
REMARK   3    B33 (A**2) : NULL                                                 
REMARK   3    B12 (A**2) : NULL                                                 
REMARK   3    B13 (A**2) : NULL                                                 
REMARK   3    B23 (A**2) : NULL                                                 
REMARK   3                                                                      
REMARK   3  ESTIMATED COORDINATE ERROR.                                         
REMARK   3   ESD FROM LUZZATI PLOT        (A) : 0.31                            
REMARK   3   ESD FROM SIGMAA              (A) : 0.35                            
REMARK   3   LOW RESOLUTION CUTOFF        (A) : 5.00                            
REMARK   3                                                                      
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.                         
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : 0.37                            
REMARK   3   ESD FROM C-V SIGMAA          (A) : 0.34                            
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.                                   
REMARK   3   BOND LENGTHS                 (A) : 0.007                           
REMARK   3   BOND ANGLES            (DEGREES) : 1.500                           
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : 22.70                           
REMARK   3   IMPROPER ANGLES        (DEGREES) : 1.310                           
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL MODEL : RESTRAINED                                
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA                
REMARK   3   MAIN-CHAIN BOND              (A**2) : NULL  ; NULL                 
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : NULL  ; NULL                 
REMARK   3   SIDE-CHAIN BOND              (A**2) : NULL  ; NULL                 
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : NULL  ; NULL                 
REMARK   3                                                                      
REMARK   3  NCS MODEL : NULL                                                    
REMARK   3                                                                      
REMARK   3  NCS RESTRAINTS.                         RMS   SIGMA/WEIGHT          
REMARK   3   GROUP  1  POSITIONAL            (A) : NULL  ; NULL                 
REMARK   3   GROUP  1  B-FACTOR           (A**2) : NULL  ; NULL                 
REMARK   3                                                                      
REMARK   3  PARAMETER FILE  1  : PARHCSDX.PRO                                   
REMARK   3  PARAMETER FILE  2  : DNA-RNA_REP.PARAM                              
REMARK   3  PARAMETER FILE  3  : PARAMETER.ELEMENTS                             
REMARK   3  PARAMETER FILE  4  : PARAMETER.ELEMENTS                             
REMARK   3  PARAMETER FILE  5  : NULL                                           
REMARK   3  TOPOLOGY FILE  1   : TOPHCSDX.PRO                                   
REMARK   3  TOPOLOGY FILE  2   : DNA-RNA.TOP                                    
REMARK   3  TOPOLOGY FILE  3   : TOPOLOGY.ELEMENTS                              
REMARK   3  TOPOLOGY FILE  4   : TOPH19.SOL                                     
REMARK   3  TOPOLOGY FILE  5   : NULL                                           
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED                   
REMARK   4                                                                      
REMARK   4 1MJM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB.                                
REMARK 100 THE DEPOSITION ID IS D_1000175027.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : AUG-96                             
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 7.0                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : N                                  
REMARK 200  RADIATION SOURCE               : ROTATING ANODE                     
REMARK 200  BEAMLINE                       : NULL                               
REMARK 200  X-RAY GENERATOR MODEL          : RIGAKU RU200                       
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.5418                             
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : MIRRORS                            
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : IMAGE PLATE                        
REMARK 200  DETECTOR MANUFACTURER          : RIGAKU RAXIS II                    
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : MOSFLM                             
REMARK 200  DATA SCALING SOFTWARE          : CCP4                               
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 60504                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.200                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 25.400                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 3.000                              
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 89.8                               
REMARK 200  DATA REDUNDANCY                : 4.400                              
REMARK 200  R MERGE                    (I) : 0.07500                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 8.0000                             
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.32                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 56.3                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 2.30                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.07500                            
REMARK 200  R SYM FOR SHELL            (I) : 0.21700                            
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 2.800                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: AMORE                                                 
REMARK 200 STARTING MODEL: PDB ENTRY 1CMA                                       
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 50.00                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN (10MG/ML) + DNA (3.8MG/ML) WAS   
REMARK 280  CRYSTALLISED FROM 8-14% P4000, 100MM CITRATE BUFFER, PH 5.0-6.0,    
REMARK 280  20% GLYCEROL, PH 7.0                                                
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21                       
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X+1/2,-Y,Z+1/2                                         
REMARK 290       3555   -X,Y+1/2,-Z+1/2                                         
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       19.98000            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       57.23500            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       32.00000            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       57.23500            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       19.98000            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       32.00000            
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 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: C, D, A, B                            
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 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                                                                      
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    ASP A  82       75.56    -69.83                                   
REMARK 500    GLU B   2      -54.52   -179.07                                   
REMARK 500    GLU B  13       77.49    -33.77                                   
REMARK 500    HIS B  14      -41.66   -158.94                                   
REMARK 500    LYS B  17      -20.69   -171.78                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 1MJ2   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 1MJO   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 1MJP   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 1MJQ   RELATED DB: PDB                                   
DBREF  1MJM A    1   104  UNP    P0A8U6   METJ_ECOLI       1    104             
DBREF  1MJM B    1   104  UNP    P0A8U6   METJ_ECOLI       1    104             
DBREF  1MJM C  401   410  PDB    1MJM     1MJM           401    410             
DBREF  1MJM D  411   420  PDB    1MJM     1MJM           411    420             
SEQADV 1MJM LYS A   44  UNP  P0A8U6    GLN    44 ENGINEERED MUTATION            
SEQADV 1MJM LYS B   44  UNP  P0A8U6    GLN    44 ENGINEERED MUTATION            
SEQRES   1 C   10   DG  DA  DG  DA  DC  DG  DT  DC  DT  DC                      
SEQRES   1 D   10   DG  DA  DG  DA  DC  DG  DT  DC  DT  DC                      
SEQRES   1 A  104  ALA GLU TRP SER GLY GLU TYR ILE SER PRO TYR ALA GLU          
SEQRES   2 A  104  HIS GLY LYS LYS SER GLU GLN VAL LYS LYS ILE THR VAL          
SEQRES   3 A  104  SER ILE PRO LEU LYS VAL LEU LYS ILE LEU THR ASP GLU          
SEQRES   4 A  104  ARG THR ARG ARG LYS VAL ASN ASN LEU ARG HIS ALA THR          
SEQRES   5 A  104  ASN SER GLU LEU LEU CYS GLU ALA PHE LEU HIS ALA PHE          
SEQRES   6 A  104  THR GLY GLN PRO LEU PRO ASP ASP ALA ASP LEU ARG LYS          
SEQRES   7 A  104  GLU ARG SER ASP GLU ILE PRO GLU ALA ALA LYS GLU ILE          
SEQRES   8 A  104  MET ARG GLU MET GLY ILE ASN PRO GLU THR TRP GLU TYR          
SEQRES   1 B  104  ALA GLU TRP SER GLY GLU TYR ILE SER PRO TYR ALA GLU          
SEQRES   2 B  104  HIS GLY LYS LYS SER GLU GLN VAL LYS LYS ILE THR VAL          
SEQRES   3 B  104  SER ILE PRO LEU LYS VAL LEU LYS ILE LEU THR ASP GLU          
SEQRES   4 B  104  ARG THR ARG ARG LYS VAL ASN ASN LEU ARG HIS ALA THR          
SEQRES   5 B  104  ASN SER GLU LEU LEU CYS GLU ALA PHE LEU HIS ALA PHE          
SEQRES   6 B  104  THR GLY GLN PRO LEU PRO ASP ASP ALA ASP LEU ARG LYS          
SEQRES   7 B  104  GLU ARG SER ASP GLU ILE PRO GLU ALA ALA LYS GLU ILE          
SEQRES   8 B  104  MET ARG GLU MET GLY ILE ASN PRO GLU THR TRP GLU TYR          
FORMUL   5  HOH   *177(H2 O)                                                    
HELIX    1  AA LEU A   30  VAL A   45  1                                  16    
HELIX    2  AB ASN A   53  THR A   66  1                                  14    
HELIX    3  AC GLU A   86  GLU A   94  1                                   9    
HELIX    4  BA LEU B   30  VAL B   45  1                                  16    
HELIX    5  BB ASN B   53  THR B   66  1                                  14    
HELIX    6  BC GLU B   86  MET B   95  1                                  10    
SHEET    1 AS1 1 VAL A  21  ILE A  28  0                                        
SHEET    1 BS2 1 VAL B  21  ILE B  28  0                                        
CRYST1   39.960   64.000  114.470  90.00  90.00  90.00 P 21 21 21    8          
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      0.025025  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.015625  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.008736        0.00000