HEADER    BIOSYNTHETIC PROTEIN                    13-JAN-23   8I1M              
TITLE     CRYSTAL STRUCTURE OF OXIDATED APSK1 DOMAIN FROM HUMAN PAPSS1 IN       
TITLE    2 COMPLEX WITH APS AND ADP                                             
CAVEAT     8I1M    ADX A 302 HAS WRONG CHIRALITY AT ATOM C2' ADX A 302 HAS      
CAVEAT   2 8I1M    WRONG CHIRALITY AT ATOM C1'                                  
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: PAPSS1 PROTEIN;                                            
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: APSK1 DOMAIN;                                              
COMPND   5 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE   3 ORGANISM_COMMON: HUMAN;                                              
SOURCE   4 ORGANISM_TAXID: 9606;                                                
SOURCE   5 GENE: PAPSS1;                                                        
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562                                         
KEYWDS    5'-PHOSPHOSULFATE KINASE 1, APSK1, HUMAN PAPSS1, BIOSYNTHETIC PROTEIN 
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    L.ZHANG,W.Y.SONG,L.ZHANG                                              
REVDAT   3   06-NOV-24 8I1M    1       REMARK                                   
REVDAT   2   19-JUL-23 8I1M    1       JRNL                                     
REVDAT   1   28-JUN-23 8I1M    0                                                
JRNL        AUTH   L.ZHANG,W.SONG,T.LI,Y.MU,P.ZHANG,J.HU,H.LIN,J.ZHANG,H.GAO,   
JRNL        AUTH 2 L.ZHANG                                                      
JRNL        TITL   REDOX SWITCHING MECHANISM OF THE ADENOSINE 5'-PHOSPHOSULFATE 
JRNL        TITL 2 KINASE DOMAIN (APSK2) OF HUMAN PAPS SYNTHASE 2.              
JRNL        REF    STRUCTURE                     V.  31   826 2023              
JRNL        REFN                   ISSN 0969-2126                               
JRNL        PMID   37207644                                                     
JRNL        DOI    10.1016/J.STR.2023.04.012                                    
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.70 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX 1.17.1                                        
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 : ML                                            
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 46.85                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.350                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 77.0                           
REMARK   3   NUMBER OF REFLECTIONS             : 15998                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.185                           
REMARK   3   R VALUE            (WORKING SET) : 0.182                           
REMARK   3   FREE R VALUE                     : 0.230                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.090                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 815                             
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 46.8480 -  3.0879    0.99     3331   171  0.1616 0.1850        
REMARK   3     2  3.0879 -  2.4510    0.99     3278   159  0.1892 0.2334        
REMARK   3     3  2.4510 -  2.1412    0.96     3143   183  0.1908 0.2628        
REMARK   3     4  2.1412 -  1.9454    0.78     2572   123  0.2016 0.2702        
REMARK   3     5  1.9454 -  1.8060    0.56     1816   113  0.2155 0.2913        
REMARK   3     6  1.8060 -  1.6995    0.33     1043    66  0.2255 0.3337        
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)     : 0.200            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.600           
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : NULL                           
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      :  0.006           1587                                  
REMARK   3   ANGLE     :  1.035           2159                                  
REMARK   3   CHIRALITY :  0.054            237                                  
REMARK   3   PLANARITY :  0.006            277                                  
REMARK   3   DIHEDRAL  : 18.377            962                                  
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 8I1M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-JAN-23.                  
REMARK 100 THE DEPOSITION ID IS D_1300034771.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 18-JAN-22                          
REMARK 200  TEMPERATURE           (KELVIN) : 180                                
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                       : BL19U1                             
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.9785                             
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : PIXEL                              
REMARK 200  DETECTOR MANUFACTURER          : DECTRIS PILATUS3 6M                
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : DENZO                              
REMARK 200  DATA SCALING SOFTWARE          : HKL-3000                           
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 18780                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.699                              
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     (%) : 90.3                               
REMARK 200  DATA REDUNDANCY                : 5.900                              
REMARK 200  R MERGE                    (I) : 1.00400                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 7.7000                             
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.76                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 56.7                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 4.20                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.46200                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : NULL                               
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: PHASER                                                
REMARK 200 STARTING MODEL: 2OFX                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 44.80                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0 M AMMONIUM SULFATE, 0.1 M HEPES,     
REMARK 280  PH7.5 AND 2% W/V PEG4000, VAPOR DIFFUSION, SITTING DROP,            
REMARK 280  TEMPERATURE 291K                                                    
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1                          
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X,Y,-Z                                                 
REMARK 290       3555   X+1/2,Y+1/2,Z                                           
REMARK 290       4555   -X+1/2,Y+1/2,-Z                                         
REMARK 290                                                                      
REMARK 290     WHERE NNN -> OPERATOR NUMBER                                     
REMARK 290           MMM -> TRANSLATION VECTOR                                  
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                            
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM             
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY                
REMARK 290 RELATED MOLECULES.                                                   
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   2  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000 -1.000000        0.00000            
REMARK 290   SMTRY1   3  1.000000  0.000000  0.000000       57.17600            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       25.68050            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   4 -1.000000  0.000000  0.000000       57.17600            
REMARK 290   SMTRY2   4  0.000000  1.000000  0.000000       25.68050            
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: DIMERIC                           
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC                    
REMARK 350 SOFTWARE USED: PISA                                                  
REMARK 350 TOTAL BURIED SURFACE AREA: 5620 ANGSTROM**2                          
REMARK 350 SURFACE AREA OF THE COMPLEX: 16000 ANGSTROM**2                       
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -65.0 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 350   BIOMT1   2 -1.000000  0.000000  0.000000        0.00000            
REMARK 350   BIOMT2   2  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   2  0.000000  0.000000 -1.000000        0.00000            
REMARK 375                                                                      
REMARK 375 SPECIAL POSITION                                                     
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS            
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL          
REMARK 375 POSITIONS.                                                           
REMARK 375                                                                      
REMARK 375 ATOM RES CSSEQI                                                      
REMARK 375      HOH A 402  LIES ON A SPECIAL POSITION.                          
REMARK 375      HOH A 553  LIES ON A SPECIAL POSITION.                          
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     ALA A    25                                                      
REMARK 465     THR A    26                                                      
REMARK 465     ASN A    27                                                      
REMARK 465     VAL A    28                                                      
REMARK 465     THR A    29                                                      
REMARK 465     TYR A    30                                                      
REMARK 465     GLN A    31                                                      
REMARK 465     ALA A    32                                                      
REMARK 465     HIS A    33                                                      
REMARK 465     HIS A    34                                                      
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    SER A 133       72.53     41.21                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
DBREF  8I1M A   25   227  UNP    Q05BW9   Q05BW9_HUMAN    25    227             
SEQADV 8I1M ASP A  191  UNP  Q05BW9    GLU   191 CONFLICT                       
SEQRES   1 A  203  ALA THR ASN VAL THR TYR GLN ALA HIS HIS VAL SER ARG          
SEQRES   2 A  203  ASN LYS ARG GLY GLN VAL VAL GLY THR ARG GLY GLY PHE          
SEQRES   3 A  203  ARG GLY CYS THR VAL TRP LEU THR GLY LEU SER GLY ALA          
SEQRES   4 A  203  GLY LYS THR THR VAL SER MET ALA LEU GLU GLU TYR LEU          
SEQRES   5 A  203  VAL CYS HIS GLY ILE PRO CYS TYR THR LEU ASP GLY ASP          
SEQRES   6 A  203  ASN ILE ARG GLN GLY LEU ASN LYS ASN LEU GLY PHE SER          
SEQRES   7 A  203  PRO GLU ASP ARG GLU GLU ASN VAL ARG ARG ILE ALA GLU          
SEQRES   8 A  203  VAL ALA LYS LEU PHE ALA ASP ALA GLY LEU VAL CYS ILE          
SEQRES   9 A  203  THR SER PHE ILE SER PRO TYR THR GLN ASP ARG ASN ASN          
SEQRES  10 A  203  ALA ARG GLN ILE HIS GLU GLY ALA SER LEU PRO PHE PHE          
SEQRES  11 A  203  GLU VAL PHE VAL ASP ALA PRO LEU HIS VAL CYS GLU GLN          
SEQRES  12 A  203  ARG ASP VAL LYS GLY LEU TYR LYS LYS ALA ARG ALA GLY          
SEQRES  13 A  203  GLU ILE LYS GLY PHE THR GLY ILE ASP SER ASP TYR GLU          
SEQRES  14 A  203  LYS PRO GLU ALA PRO GLU LEU VAL LEU LYS THR ASP SER          
SEQRES  15 A  203  CYS ASP VAL ASN ASP CYS VAL GLN GLN VAL VAL GLU LEU          
SEQRES  16 A  203  LEU GLN GLU ARG ASP ILE VAL PRO                              
HET    ADP  A 301      27                                                       
HET    ADX  A 302      27                                                       
HET    PO4  A 303       5                                                       
HETNAM     ADP ADENOSINE-5'-DIPHOSPHATE                                         
HETNAM     ADX ADENOSINE-5'-PHOSPHOSULFATE                                      
HETNAM     PO4 PHOSPHATE ION                                                    
FORMUL   2  ADP    C10 H15 N5 O10 P2                                            
FORMUL   3  ADX    C10 H14 N5 O10 P S                                           
FORMUL   4  PO4    O4 P 3-                                                      
FORMUL   5  HOH   *156(H2 O)                                                    
HELIX    1 AA1 SER A   36  VAL A   44  1                                   9    
HELIX    2 AA2 GLY A   64  HIS A   79  1                                  16    
HELIX    3 AA3 GLY A   88  ARG A   92  1                                   5    
HELIX    4 AA4 SER A  102  ALA A  123  1                                  22    
HELIX    5 AA5 TYR A  135  ALA A  149  1                                  15    
HELIX    6 AA6 PRO A  161  ASP A  169  1                                   9    
HELIX    7 AA7 GLY A  172  ALA A  179  1                                   8    
HELIX    8 AA8 ASP A  208  ARG A  223  1                                  16    
SHEET    1 AA1 5 CYS A  83  ASP A  87  0                                        
SHEET    2 AA1 5 VAL A 126  SER A 130  1  O  ILE A 128   N  LEU A  86           
SHEET    3 AA1 5 CYS A  53  THR A  58  1  N  CYS A  53   O  CYS A 127           
SHEET    4 AA1 5 PHE A 153  VAL A 158  1  O  VAL A 156   N  TRP A  56           
SHEET    5 AA1 5 LEU A 200  LEU A 202  1  O  LEU A 202   N  PHE A 157           
SSBOND   1 CYS A  207    CYS A  212                          1555   1555  2.04  
CRYST1  114.352   51.361   32.397  90.00  91.94  90.00 C 1 2 1       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      0.008745  0.000000  0.000295        0.00000                         
SCALE2      0.000000  0.019470  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.030885        0.00000