HEADER    OXYGEN STORAGE                          29-OCT-20   7DDR              
TITLE     ANCESTRAL MYOGLOBIN AMBSP OF PUIJILA DARWINI RELATIVE (IMIDAZOL       
TITLE    2 LIGAND)                                                              
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: ANCESTRAL MYOGLOBIN AMBSP;                                 
COMPND   3 CHAIN: A;                                                            
COMPND   4 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;                            
SOURCE   3 ORGANISM_TAXID: 32630;                                               
SOURCE   4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   5 EXPRESSION_SYSTEM_TAXID: 562                                         
KEYWDS    PROTEIN EVOLUTION, ANCESTRAL PROTEIN, DIVING ADAPTATION, SEALS,       
KEYWDS   2 OXYGEN STORAGE                                                       
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    Y.ISOGAI,H.IMAMURA,S.NAKAE,T.SUMI,K.TAKAHASHI,T.SHIRAI                
REVDAT   2   29-NOV-23 7DDR    1       REMARK                                   
REVDAT   1   08-SEP-21 7DDR    0                                                
JRNL        AUTH   Y.ISOGAI,H.IMAMURA,S.NAKAE,T.SUMI,K.I.TAKAHASHI,T.SHIRAI     
JRNL        TITL   COMMON AND UNIQUE STRATEGIES OF MYOGLOBIN EVOLUTION FOR      
JRNL        TITL 2 DEEP-SEA ADAPTATION OF DIVING MAMMALS.                       
JRNL        REF    ISCIENCE                      V.  24 02920 2021              
JRNL        REFN                   ESSN 2589-0042                               
JRNL        PMID   34430810                                                     
JRNL        DOI    10.1016/J.ISCI.2021.102920                                   
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.50 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX 1.17RC5_3630                                  
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) : 1.50                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 20.00                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.340                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.6                           
REMARK   3   NUMBER OF REFLECTIONS             : 19093                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.166                           
REMARK   3   R VALUE            (WORKING SET) : 0.164                           
REMARK   3   FREE R VALUE                     : 0.202                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.040                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 963                             
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 19.9200 -  2.8700    1.00     2744   146  0.1509 0.1803        
REMARK   3     2  2.8700 -  2.2800    1.00     2640   126  0.1451 0.1569        
REMARK   3     3  2.2800 -  1.9900    1.00     2598   120  0.1464 0.1776        
REMARK   3     4  1.9900 -  1.8100    0.99     2549   144  0.1646 0.2184        
REMARK   3     5  1.8100 -  1.6800    0.99     2563   115  0.2022 0.3074        
REMARK   3     6  1.6800 -  1.5800    0.99     2544   137  0.2286 0.2750        
REMARK   3     7  1.5800 -  1.5000    0.99     2492   175  0.2628 0.3132        
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)     : 0.178            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.820           
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 13.96                          
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 17.46                          
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      :  0.014           1318                                  
REMARK   3   ANGLE     :  1.302           1785                                  
REMARK   3   CHIRALITY :  0.069            180                                  
REMARK   3   PLANARITY :  0.007            228                                  
REMARK   3   DIHEDRAL  : 25.214            494                                  
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 7DDR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-NOV-20.                  
REMARK 100 THE DEPOSITION ID IS D_1300019200.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 11-MAY-19                          
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               : SPRING-8                           
REMARK 200  BEAMLINE                       : BL26B1                             
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.0000                             
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : PIXEL                              
REMARK 200  DETECTOR MANUFACTURER          : DECTRIS EIGER2 X 4M                
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : MOSFLM                             
REMARK 200  DATA SCALING SOFTWARE          : SCALA                              
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 19228                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.500                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 20.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.9                               
REMARK 200  DATA REDUNDANCY                : 2.000                              
REMARK 200  R MERGE                    (I) : 0.01000                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 18.3000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.58                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : NULL                               
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.04000                            
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: PHENIX 1.17RC5_3630                                   
REMARK 200 STARTING MODEL: 5YCE                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 26.69                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.68                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MIB BUFFER PH 5, 25% W/V PEG        
REMARK 280  1500, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K               
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       14.01000            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       32.76000            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       31.36000            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       32.76000            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       14.01000            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       31.36000            
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: 1080 ANGSTROM**2                          
REMARK 350 SURFACE AREA OF THE COMPLEX: 8150 ANGSTROM**2                        
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 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       71.05   -156.02                                   
REMARK 500    GLN A  81       73.16   -100.01                                   
REMARK 500    THR A  95      -88.27   -113.98                                   
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   89.2                                              
REMARK 620 3 HEM A 201   NB   88.3  88.2                                        
REMARK 620 4 HEM A 201   NC   92.1 177.6  89.8                                  
REMARK 620 5 HEM A 201   ND   92.3  91.8 179.4  90.2                            
REMARK 620 6 IMD A 202   N1  173.8  97.0  92.3  81.7  87.1                      
REMARK 620 N                    1     2     3     4     5                       
DBREF  7DDR A    0   153  PDB    7DDR     7DDR             0    153             
SEQRES   1 A  154  MET GLY LEU SER ASP GLY GLU TRP GLN LEU VAL LEU ASN          
SEQRES   2 A  154  VAL TRP GLY LYS VAL GLU ALA ASP LEU ALA GLY HIS GLY          
SEQRES   3 A  154  GLN GLU VAL LEU ILE ARG LEU PHE LYS GLY HIS PRO GLU          
SEQRES   4 A  154  THR LEU GLU LYS PHE ASP LYS PHE LYS HIS LEU LYS SER          
SEQRES   5 A  154  GLU ASP GLU MET LYS GLY SER GLU ASP LEU LYS LYS HIS          
SEQRES   6 A  154  GLY ASN THR VAL LEU THR ALA LEU GLY GLY ILE LEU LYS          
SEQRES   7 A  154  LYS LYS GLY GLN HIS GLU ALA GLU LEU LYS PRO LEU ALA          
SEQRES   8 A  154  GLN SER HIS ALA THR LYS HIS LYS ILE PRO VAL LYS TYR          
SEQRES   9 A  154  LEU GLU PHE ILE SER ASP ALA ILE ILE GLN VAL LEU GLN          
SEQRES  10 A  154  SER LYS HIS PRO GLY ASP PHE GLY ALA ASP ALA GLN ALA          
SEQRES  11 A  154  ALA MET LYS LYS ALA LEU GLU LEU PHE ARG ASN ASP ILE          
SEQRES  12 A  154  ALA ALA LYS TYR LYS GLU LEU GLY PHE GLN GLY                  
HET    HEM  A 201      82                                                       
HET    IMD  A 202       9                                                       
HETNAM     HEM PROTOPORPHYRIN IX CONTAINING FE                                  
HETNAM     IMD IMIDAZOLE                                                        
HETSYN     HEM HEME                                                             
FORMUL   2  HEM    C34 H32 FE N4 O4                                             
FORMUL   3  IMD    C3 H5 N2 1+                                                  
FORMUL   4  HOH   *136(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 LYS A   45  GLU A   52  1                                   8    
HELIX    5 AA5 SER A   58  LYS A   78  1                                  21    
HELIX    6 AA6 HIS A   82  THR A   95  1                                  14    
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  2.18  
LINK        FE   HEM A 201                 N1  IMD A 202     1555   1555  2.17  
CRYST1   28.020   62.720   65.520  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      0.035689  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.015944  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.015263        0.00000