HEADER    OXYGEN STORAGE                          25-MAR-22   7XCQ              
TITLE     X-RAY CRYSTAL STRUCTURE OF SPERM WHALE MYOGLOBIN H64D MUTANT          
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: MYOGLOBIN;                                                 
COMPND   3 CHAIN: A;                                                            
COMPND   4 ENGINEERED: YES;                                                     
COMPND   5 MUTATION: YES                                                        
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: PHYSETER CATODON;                               
SOURCE   3 ORGANISM_COMMON: SPERM WHALE;                                        
SOURCE   4 ORGANISM_TAXID: 9755;                                                
SOURCE   5 GENE: MB;                                                            
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562                                         
KEYWDS    SPERM WHALE MYOGLOBIN, OXYGEN STORAGE                                 
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    Y.W.LIN                                                               
REVDAT   2   29-NOV-23 7XCQ    1       REMARK                                   
REVDAT   1   29-MAR-23 7XCQ    0                                                
JRNL        AUTH   Y.W.LIN                                                      
JRNL        TITL   X-RAY CRYSTAL STRUCTURE OF SPERM WHALE MYOGLOBIN H64D MUTANT 
JRNL        REF    TO BE PUBLISHED                                              
JRNL        REFN                                                                
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.60 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX 1.18.1_3865                                   
REMARK   3   AUTHORS     : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN            
REMARK   3               : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,           
REMARK   3               : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,            
REMARK   3               : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,              
REMARK   3               : REETAL PAI,RANDY READ,JANE RICHARDSON,               
REMARK   3               : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,           
REMARK   3               : NICHOLAS SAUTER,JACOB SMITH,LAURENT                  
REMARK   3               : STORONI,TOM TERWILLIGER,PETER ZWART                  
REMARK   3                                                                      
REMARK   3    REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2           
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 24.15                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.350                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 100.0                          
REMARK   3   NUMBER OF REFLECTIONS             : 20645                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.179                           
REMARK   3   R VALUE            (WORKING SET) : 0.178                           
REMARK   3   FREE R VALUE                     : 0.189                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 4.940                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 1020                            
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT (IN BINS).                           
REMARK   3   BIN  RESOLUTION RANGE  COMPL.    NWORK NFREE   RWORK  RFREE        
REMARK   3     1 24.1500 -  3.0600    1.00     2953   155  0.1731 0.1572        
REMARK   3     2  3.0600 -  2.4300    1.00     2830   143  0.1809 0.1925        
REMARK   3     3  2.4300 -  2.1200    1.00     2793   146  0.1672 0.1937        
REMARK   3     4  2.1200 -  1.9300    1.00     2772   148  0.1779 0.2118        
REMARK   3     5  1.9300 -  1.7900    1.00     2752   154  0.1892 0.2222        
REMARK   3     6  1.7900 -  1.6800    1.00     2756   136  0.1894 0.2377        
REMARK   3     7  1.6800 -  1.6000    1.00     2769   138  0.2012 0.2220        
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELLING.                                             
REMARK   3   METHOD USED        : FLAT BULK SOLVENT MODEL                       
REMARK   3   SOLVENT RADIUS     : 1.11                                          
REMARK   3   SHRINKAGE RADIUS   : 0.90                                          
REMARK   3   K_SOL              : NULL                                          
REMARK   3   B_SOL              : NULL                                          
REMARK   3                                                                      
REMARK   3  ERROR ESTIMATES.                                                    
REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.117            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.916           
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 15.08                          
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 19.54                          
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  TWINNING INFORMATION.                                               
REMARK   3   FRACTION: NULL                                                     
REMARK   3   OPERATOR: NULL                                                     
REMARK   3                                                                      
REMARK   3  DEVIATIONS FROM IDEAL VALUES.                                       
REMARK   3                 RMSD          COUNT                                  
REMARK   3   BOND      :  0.008           1295                                  
REMARK   3   ANGLE     :  1.157           1754                                  
REMARK   3   CHIRALITY :  0.070            182                                  
REMARK   3   PLANARITY :  0.005            217                                  
REMARK   3   DIHEDRAL  : 20.092            470                                  
REMARK   3                                                                      
REMARK   3  TLS DETAILS                                                         
REMARK   3   NUMBER OF TLS GROUPS  : NULL                                       
REMARK   3                                                                      
REMARK   3  NCS DETAILS                                                         
REMARK   3   NUMBER OF NCS GROUPS : NULL                                        
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 7XCQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-APR-22.                  
REMARK 100 THE DEPOSITION ID IS D_1300028552.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 10-NOV-21                          
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               : SSRF                               
REMARK 200  BEAMLINE                       : BL02U1                             
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.9791                             
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : PIXEL                              
REMARK 200  DETECTOR MANUFACTURER          : DECTRIS PILATUS 6M                 
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : XIA2                               
REMARK 200  DATA SCALING SOFTWARE          : XIA2                               
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 20645                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.600                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 50.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.9                               
REMARK 200  DATA REDUNDANCY                : 12.70                              
REMARK 200  R MERGE                    (I) : 0.09200                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 19.8400                            
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) : 1.66                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : NULL                               
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.53100                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 6.930                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: MOLREP                                                
REMARK 200 STARTING MODEL: 1MTJ                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 43.55                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, VAPOR DIFFUSION, HANGING       
REMARK 280  DROP, TEMPERATURE 293K                                              
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       19.87000            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       38.72000            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       24.56000            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       38.72000            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       19.87000            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       24.56000            
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: MONOMERIC                         
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC                  
REMARK 350 SOFTWARE USED: PISA                                                  
REMARK 350 TOTAL BURIED SURFACE AREA: 1130 ANGSTROM**2                          
REMARK 350 SURFACE AREA OF THE COMPLEX: 7970 ANGSTROM**2                        
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL                        
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 465                                                                      
REMARK 465 MISSING RESIDUES                                                     
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE                       
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)                
REMARK 465                                                                      
REMARK 465   M RES C SSSEQI                                                     
REMARK 465     MET A     0                                                      
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT                     
REMARK 500                                                                      
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.                            
REMARK 500                                                                      
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE          
REMARK 500   O    HOH A   458     O    HOH A   488              1.90            
REMARK 500   O    HOH A   469     O    HOH A   474              2.06            
REMARK 500   NE2  GLN A    91     O    HOH A   301              2.10            
REMARK 500   OE2  GLU A    59     O    HOH A   302              2.10            
REMARK 500   O    HOH A   317     O    HOH A   441              2.16            
REMARK 500   O    HOH A   385     O    HOH A   387              2.19            
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: CLOSE CONTACTS                                             
REMARK 500                                                                      
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC             
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT.  AN ATOM LOCATED WITHIN 0.15          
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A           
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375             
REMARK 500 INSTEAD OF REMARK 500.  ATOMS WITH NON-BLANK ALTERNATE               
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.            
REMARK 500                                                                      
REMARK 500 DISTANCE CUTOFF:                                                     
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS              
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS                  
REMARK 500                                                                      
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI  SSYMOP   DISTANCE          
REMARK 500   O    HOH A   336     O    HOH A   355     4555     2.18            
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                                                                      
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  20       69.74   -153.55                                   
REMARK 500    PHE A  46       19.42   -140.05                                   
REMARK 500    LYS A  96      -60.52   -108.71                                   
REMARK 500    PHE A 123       49.96   -146.94                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 620                                                                      
REMARK 620 METAL COORDINATION                                                   
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):                             
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                             HEM A 201  FE                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 HIS A  93   NE2                                                    
REMARK 620 2 HEM A 201   NA   91.9                                              
REMARK 620 3 HEM A 201   NB   94.3  88.0                                        
REMARK 620 4 HEM A 201   NC  102.0 166.1  90.8                                  
REMARK 620 5 HEM A 201   ND  100.3  90.4 165.3  87.2                            
REMARK 620 N                    1     2     3     4                             
DBREF  7XCQ A    0   153  UNP    P02185   MYG_PHYMC        1    154             
SEQADV 7XCQ ASP A   64  UNP  P02185    HIS    65 ENGINEERED MUTATION            
SEQRES   1 A  154  MET VAL LEU SER GLU GLY GLU TRP GLN LEU VAL LEU HIS          
SEQRES   2 A  154  VAL TRP ALA LYS VAL GLU ALA ASP VAL ALA GLY HIS GLY          
SEQRES   3 A  154  GLN ASP ILE LEU ILE ARG LEU PHE LYS SER HIS PRO GLU          
SEQRES   4 A  154  THR LEU GLU LYS PHE ASP ARG PHE LYS HIS LEU LYS THR          
SEQRES   5 A  154  GLU ALA GLU MET LYS ALA SER GLU ASP LEU LYS LYS ASP          
SEQRES   6 A  154  GLY VAL THR VAL LEU THR ALA LEU GLY ALA ILE LEU LYS          
SEQRES   7 A  154  LYS LYS GLY HIS HIS GLU ALA GLU LEU LYS PRO LEU ALA          
SEQRES   8 A  154  GLN SER HIS ALA THR LYS HIS LYS ILE PRO ILE LYS TYR          
SEQRES   9 A  154  LEU GLU PHE ILE SER GLU ALA ILE ILE HIS VAL LEU HIS          
SEQRES  10 A  154  SER ARG HIS PRO GLY ASP PHE GLY ALA ASP ALA GLN GLY          
SEQRES  11 A  154  ALA MET ASN LYS ALA LEU GLU LEU PHE ARG LYS ASP ILE          
SEQRES  12 A  154  ALA ALA LYS TYR LYS GLU LEU GLY TYR GLN GLY                  
HET    HEM  A 201      43                                                       
HETNAM     HEM PROTOPORPHYRIN IX CONTAINING FE                                  
HETSYN     HEM HEME                                                             
FORMUL   2  HEM    C34 H32 FE N4 O4                                             
FORMUL   3  HOH   *193(H2 O)                                                    
HELIX    1 AA1 SER A    3  ALA A   19  1                                  17    
HELIX    2 AA2 ASP A   20  HIS A   36  1                                  17    
HELIX    3 AA3 PRO A   37  PHE A   43  5                                   7    
HELIX    4 AA4 THR A   51  SER A   58  1                                   8    
HELIX    5 AA5 SER A   58  LYS A   78  1                                  21    
HELIX    6 AA6 HIS A   82  LYS A   96  1                                  15    
HELIX    7 AA7 PRO A  100  HIS A  119  1                                  20    
HELIX    8 AA8 PRO A  120  PHE A  123  5                                   4    
HELIX    9 AA9 GLY A  124  LEU A  149  1                                  26    
LINK         NE2 HIS A  93                FE   HEM A 201     1555   1555  2.22  
CRYST1   39.740   49.120   77.440  90.00  90.00  90.00 P 21 21 21    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      0.025164  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.020358  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.012913        0.00000