HEADER    RNA BINDING PROTEIN                     09-FEB-21   7NH2              
TITLE     CRYSTAL STRUCTURE OF TOXOPLASMA CPSF4-YTH DOMAIN BOUND TO M6A         
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: ZINC FINGER (CCCH TYPE) MOTIF-CONTAINING PROTEIN;          
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: CPSF4;                                                      
COMPND   5 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: TOXOPLASMA GONDII (STRAIN ATCC 50611 / ME49);   
SOURCE   3 ORGANISM_TAXID: 508771;                                              
SOURCE   4 STRAIN: ATCC 50611 / ME49;                                           
SOURCE   5 GENE: TGME49_201200;                                                 
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: BL21-RIL                                   
KEYWDS    YTH, CLEAVAGE AND POLYADENYLATION, RNA, M6A, RNA BINDING PROTEIN      
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    C.SWALE,M.W.BOWLER                                                    
REVDAT   3   31-JAN-24 7NH2    1       REMARK                                   
REVDAT   2   28-JUL-21 7NH2    1       JRNL                                     
REVDAT   1   21-JUL-21 7NH2    0                                                
JRNL        AUTH   D.C.FARHAT,M.W.BOWLER,G.COMMUNIE,D.PONTIER,L.BELMUDES,C.MAS, 
JRNL        AUTH 2 C.CORRAO,Y.COUTE,A.BOUGDOUR,T.LAGRANGE,M.A.HAKIMI,C.SWALE    
JRNL        TITL   A PLANT-LIKE MECHANISM COUPLING M6A READING TO               
JRNL        TITL 2 POLYADENYLATION SAFEGUARDS TRANSCRIPTOME INTEGRITY AND       
JRNL        TITL 3 DEVELOPMENTAL GENE PARTITIONING IN TOXOPLASMA .              
JRNL        REF    ELIFE                         V.  10       2021              
JRNL        REFN                   ESSN 2050-084X                               
JRNL        PMID   34263725                                                     
JRNL        DOI    10.7554/ELIFE.68312                                          
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.35 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX 1.17.1_3660                                   
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) : 1.35                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 30.76                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.960                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 92.7                           
REMARK   3   NUMBER OF REFLECTIONS             : 30007                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.183                           
REMARK   3   R VALUE            (WORKING SET) : 0.183                           
REMARK   3   FREE R VALUE                     : 0.197                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.110                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 1532                            
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 30.7600 -  3.0000    0.98     2723   151  0.1748 0.1893        
REMARK   3     2  3.0000 -  2.3800    0.94     2618   152  0.1813 0.1829        
REMARK   3     3  2.3800 -  2.0800    0.94     2631   148  0.1618 0.1849        
REMARK   3     4  2.0800 -  1.8900    0.93     2584   149  0.1638 0.1745        
REMARK   3     5  1.8900 -  1.7500    0.94     2631   131  0.1778 0.1991        
REMARK   3     6  1.7500 -  1.6500    0.94     2630   151  0.1776 0.1976        
REMARK   3     7  1.6500 -  1.5700    0.92     2607   131  0.1947 0.2316        
REMARK   3     8  1.5700 -  1.5000    0.91     2504   135  0.2107 0.2377        
REMARK   3     9  1.5000 -  1.4400    0.91     2560   123  0.2174 0.2229        
REMARK   3    10  1.4400 -  1.3900    0.90     2531   122  0.2296 0.2279        
REMARK   3    11  1.3900 -  1.3500    0.88     2456   139  0.2416 0.2609        
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)     : 0.139            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.998           
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 9.18                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 13.21                          
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      :  0.005           1298                                  
REMARK   3   ANGLE     :  0.822           1762                                  
REMARK   3   CHIRALITY :  0.077            185                                  
REMARK   3   PLANARITY :  0.004            227                                  
REMARK   3   DIHEDRAL  : 15.807            485                                  
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 7NH2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-FEB-21.                  
REMARK 100 THE DEPOSITION ID IS D_1292113920.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 26-SEP-18                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 4.5                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : ESRF                               
REMARK 200  BEAMLINE                       : MASSIF-1                           
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.9660                             
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : PIXEL                              
REMARK 200  DETECTOR MANUFACTURER          : DECTRIS PILATUS3 2M                
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : XIA2, DIALS                        
REMARK 200  DATA SCALING SOFTWARE          : DIALS                              
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 30036                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.349                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 30.760                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 92.6                               
REMARK 200  DATA REDUNDANCY                : 1.600                              
REMARK 200  R MERGE                    (I) : NULL                               
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 6.6000                             
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.40                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 88.4                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 1.70                               
REMARK 200  R MERGE FOR SHELL          (I) : NULL                               
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 2.100                              
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: 4R3I                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 40.25                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 50% PEG 400, 0.1M SODIUM ACETATE PH      
REMARK 280  4.5 AND 0.2M LISO4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE      
REMARK 280  293K                                                                
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1                              
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,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                                                                      
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: 390 ANGSTROM**2                           
REMARK 350 SURFACE AREA OF THE COMPLEX: 7810 ANGSTROM**2                        
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 7.0 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     GLY A   433                                                      
REMARK 465     ASP A   434                                                      
REMARK 465     PRO A   435                                                      
REMARK 465     PHE A   436                                                      
REMARK 465     GLY A   437                                                      
REMARK 465     HIS A   438                                                      
REMARK 465     VAL A   439                                                      
REMARK 465     ALA A   440                                                      
REMARK 465     SER A   441                                                      
REMARK 465     GLY A   592                                                      
REMARK 465     ILE A   593                                                      
REMARK 465     ASP A   594                                                      
REMARK 465     PRO A   595                                                      
REMARK 465     ALA A   596                                                      
REMARK 465     THR A   597                                                      
REMARK 465     ARG A   598                                                      
REMARK 525                                                                      
REMARK 525 SOLVENT                                                              
REMARK 525                                                                      
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT                    
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST                  
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT                 
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE                       
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;                             
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE                  
REMARK 525 NUMBER; I=INSERTION CODE):                                           
REMARK 525                                                                      
REMARK 525  M RES CSSEQI                                                        
REMARK 525    HOH A 847        DISTANCE =  6.05 ANGSTROMS                       
REMARK 525    HOH A 848        DISTANCE =  6.68 ANGSTROMS                       
REMARK 610                                                                      
REMARK 610 MISSING HETEROATOM                                                   
REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;           
REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;          
REMARK 610 I=INSERTION CODE):                                                   
REMARK 610   M RES C SSEQI                                                      
REMARK 610     PG4 A  601                                                       
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 601                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue OYK A 602                 
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 7NG2   RELATED DB: PDB                                   
REMARK 900 SAME CONSTRUCT AS 7NG2 BUT BOUND TO M6A                              
DBREF  7NH2 A  434   598  UNP    S8F6K2   S8F6K2_TOXGM   434    598             
SEQADV 7NH2 GLY A  433  UNP  S8F6K2              EXPRESSION TAG                 
SEQRES   1 A  166  GLY ASP PRO PHE GLY HIS VAL ALA SER PRO GLN SER THR          
SEQRES   2 A  166  LYS ARG PHE PHE ILE ILE LYS SER ASN ARG MET SER ASN          
SEQRES   3 A  166  ILE TYR THR SER ILE GLN HIS GLY VAL TRP ALA THR SER          
SEQRES   4 A  166  LYS GLY ASN SER ARG LYS LEU SER ASN ALA PHE THR SER          
SEQRES   5 A  166  THR ASP HIS VAL LEU LEU LEU PHE SER ALA ASN GLU SER          
SEQRES   6 A  166  GLY GLY PHE GLN GLY PHE GLY ARG MET MET SER LEU PRO          
SEQRES   7 A  166  ASP PRO GLN LEU PHE PRO GLY ILE TRP GLY PRO VAL GLN          
SEQRES   8 A  166  LEU ARG LEU GLY SER ASN PHE ARG VAL MET TRP LEU LYS          
SEQRES   9 A  166  GLN CYS LYS ILE GLU PHE GLU GLU LEU GLY LYS VAL THR          
SEQRES  10 A  166  ASN PRO TRP ASN ASP ASP LEU PRO LEU ARG LYS SER ARG          
SEQRES  11 A  166  ASP GLY THR GLU VAL PRO PRO ALA LEU GLY SER LEU LEU          
SEQRES  12 A  166  CYS THR TRP MET SER GLN ARG PRO SER GLU ASP LEU LEU          
SEQRES  13 A  166  ALA GLY THR GLY ILE ASP PRO ALA THR ARG                      
HET    PG4  A 601      11                                                       
HET    OYK  A 602      12                                                       
HETNAM     PG4 TETRAETHYLENE GLYCOL                                             
HETNAM     OYK ~{N},9-DIMETHYLPURIN-6-AMINE                                     
FORMUL   2  PG4    C8 H18 O5                                                    
FORMUL   3  OYK    C7 H9 N5                                                     
FORMUL   4  HOH   *148(H2 O)                                                    
HELIX    1 AA1 ARG A  455  GLY A  466  1                                  12    
HELIX    2 AA2 SER A  471  SER A  484  1                                  14    
HELIX    3 AA3 GLY A  520  LEU A  526  5                                   7    
HELIX    4 AA4 GLU A  543  GLY A  546  5                                   4    
HELIX    5 AA5 PRO A  557  SER A  561  5                                   5    
HELIX    6 AA6 PRO A  568  GLN A  581  1                                  14    
SHEET    1 AA1 6 VAL A 467  TRP A 468  0                                        
SHEET    2 AA1 6 PHE A 530  GLU A 541 -1  O  PHE A 530   N  TRP A 468           
SHEET    3 AA1 6 GLY A 499  MET A 506 -1  N  ARG A 505   O  MET A 533           
SHEET    4 AA1 6 THR A 485  ALA A 494 -1  N  LEU A 490   O  GLY A 504           
SHEET    5 AA1 6 SER A 444  SER A 453  1  N  ARG A 447   O  LEU A 489           
SHEET    6 AA1 6 THR A 565  VAL A 567 -1  O  THR A 565   N  ILE A 450           
SITE     1 AC1  3 LYS A 446  SER A 573  HOH A 758                               
SITE     1 AC2 14 GLN A 443  ASN A 454  TRP A 468  ALA A 469                    
SITE     2 AC2 14 THR A 470  TRP A 519  VAL A 522  LEU A 526                    
SITE     3 AC2 14 ASP A 563  HOH A 710  HOH A 731  HOH A 732                    
SITE     4 AC2 14 HOH A 740  HOH A 836                                          
CRYST1   32.474   35.221   38.177 114.51 100.44  97.77 P 1           1          
ORIGX1      1.000000  0.000000  0.000000        0.00000                         
ORIGX2      0.000000  1.000000  0.000000        0.00000                         
ORIGX3      0.000000  0.000000  1.000000        0.00000                         
SCALE1      0.030794  0.004200  0.008475        0.00000                         
SCALE2      0.000000  0.028655  0.014474        0.00000                         
SCALE3      0.000000  0.000000  0.029839        0.00000