HEADER    HYDROLASE                               15-NOV-19   6TG6              
TITLE     TOPRIM DOMAIN OF RNASE M5                                             
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: RIBONUCLEASE M5;                                           
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: RNASE M5,RIBOSOMAL RNA TERMINAL MATURASE M5;                
COMPND   5 EC: 3.1.26.8;                                                        
COMPND   6 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS;                 
SOURCE   3 ORGANISM_TAXID: 1422;                                                
SOURCE   4 GENE: RNMV_1, RNMV, AVP43_02013;                                     
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 562                                         
KEYWDS    RNASE M5, RNASE, RRNA, 5S RRNA, PRECURSOR RRNA, PRE-5S RRNA,          
KEYWDS   2 RIBOSOMAL RNA, RIBONUCLEASE, CATALYTIC DOMAIN, TOPRIM DOMAIN,        
KEYWDS   3 HYDROLASE                                                            
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    S.OERUM,M.CATALA,C.TISNE                                              
REVDAT   4   01-MAY-24 6TG6    1       REMARK                                   
REVDAT   3   28-OCT-20 6TG6    1       JRNL                                     
REVDAT   2   14-OCT-20 6TG6    1       JRNL                                     
REVDAT   1   23-SEP-20 6TG6    0                                                
JRNL        AUTH   S.OERUM,T.DENDOOVEN,M.CATALA,L.GILET,C.DEGUT,A.TRINQUIER,    
JRNL        AUTH 2 M.BOURGUET,P.BARRAUD,S.CIANFERANI,B.F.LUISI,C.CONDON,C.TISNE 
JRNL        TITL   STRUCTURES OF B. SUBTILIS MATURATION RNASES CAPTURED ON 50S  
JRNL        TITL 2 RIBOSOME WITH PRE-RRNAS.                                     
JRNL        REF    MOL.CELL                      V.  80   227 2020              
JRNL        REFN                   ISSN 1097-2765                               
JRNL        PMID   32991829                                                     
JRNL        DOI    10.1016/J.MOLCEL.2020.09.008                                 
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.30 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX 1.16_3549                                     
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 : NULL                                          
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 40.55                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.350                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 98.7                           
REMARK   3   NUMBER OF REFLECTIONS             : 23306                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.193                           
REMARK   3   R VALUE            (WORKING SET) : 0.192                           
REMARK   3   FREE R VALUE                     : 0.201                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 4.990                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 1163                            
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 40.5500 -  2.5946    0.97     2916   151  0.2063 0.2053        
REMARK   3     2  2.5946 -  2.0594    0.99     2817   149  0.1921 0.1990        
REMARK   3     3  2.0594 -  1.7991    1.00     2772   146  0.1634 0.1852        
REMARK   3     4  1.7991 -  1.6346    1.00     2782   145  0.1742 0.1823        
REMARK   3     5  1.6346 -  1.5174    1.00     2753   145  0.1692 0.2042        
REMARK   3     6  1.5174 -  1.4279    1.00     2763   146  0.1784 0.1921        
REMARK   3     7  1.4279 -  1.3564    1.00     2742   144  0.2020 0.2257        
REMARK   3     8  1.3564 -  1.3000    0.95     2598   137  0.2381 0.2622        
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELLING.                                             
REMARK   3   METHOD USED        : NULL                                          
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)     : 0.110            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.040           
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 18.62                          
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      :   NULL           NULL                                  
REMARK   3   ANGLE     :   NULL           NULL                                  
REMARK   3   CHIRALITY :   NULL           NULL                                  
REMARK   3   PLANARITY :   NULL           NULL                                  
REMARK   3   DIHEDRAL  :   NULL           NULL                                  
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 6TG6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-NOV-19.                  
REMARK 100 THE DEPOSITION ID IS D_1292105404.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 25-JAN-18                          
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               : SOLEIL                             
REMARK 200  BEAMLINE                       : PROXIMA 2                          
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.9786                             
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CCD                                
REMARK 200  DETECTOR MANUFACTURER          : ADSC QUANTUM 315R                  
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : XDS                                
REMARK 200  DATA SCALING SOFTWARE          : AIMLESS                            
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 23385                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.297                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 40.550                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 98.7                               
REMARK 200  DATA REDUNDANCY                : 8.000                              
REMARK 200  R MERGE                    (I) : 0.04920                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 20.2800                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.34                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 93.3                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 4.90                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.46000                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 2.760                              
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: HOMOLOGY MODEL                                       
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 33.08                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 1.4 M SODIUM         
REMARK 280  CITRATE TRIBASIC DIHYDRATE, VAPOR DIFFUSION, SITTING DROP,          
REMARK 280  TEMPERATURE 293K                                                    
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2                        
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       18.98500            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       40.55000            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000        0.00000            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       18.98500            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       40.55000            
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: 0 ANGSTROM**2                             
REMARK 350 SURFACE AREA OF THE COMPLEX: 6660 ANGSTROM**2                        
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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            
DBREF1 6TG6 A    1   113  UNP                  A0A161UFV3_GEOSE                 
DBREF2 6TG6 A     A0A161UFV3                         34         146             
SEQADV 6TG6 GLY A   -2  UNP  A0A161UFV           EXPRESSION TAG                 
SEQADV 6TG6 GLY A   -1  UNP  A0A161UFV           EXPRESSION TAG                 
SEQADV 6TG6 SER A    0  UNP  A0A161UFV           EXPRESSION TAG                 
SEQRES   1 A  116  GLY GLY SER MET LYS ILE LYS GLU VAL ILE VAL VAL GLU          
SEQRES   2 A  116  GLY LYS ASP ASP THR ALA ALA ILE ARG ARG ALA VAL ASP          
SEQRES   3 A  116  ALA ASP THR ILE GLU THR ASN GLY ALA ALA VAL GLY ALA          
SEQRES   4 A  116  GLU VAL ILE GLU ARG ILE LYS LEU ALA LYS GLU ARG ARG          
SEQRES   5 A  116  GLY VAL ILE ILE PHE THR ASP PRO ASP PHE PRO GLY GLU          
SEQRES   6 A  116  LYS ILE ARG ARG THR ILE ALA GLU GLN VAL PRO GLY CYS          
SEQRES   7 A  116  LYS HIS ALA PHE LEU PRO ARG GLU ALA ALA LYS ALA ARG          
SEQRES   8 A  116  SER GLY LYS GLY ILE GLY VAL GLU HIS ALA SER PRO ASP          
SEQRES   9 A  116  ASP ILE ARG GLN ALA LEU ALA ASN VAL TYR GLU GLU              
FORMUL   2  HOH   *98(H2 O)                                                     
HELIX    1 AA1 GLY A   11  ARG A   20  1                                  10    
HELIX    2 AA2 GLY A   35  GLY A   50  1                                  16    
HELIX    3 AA3 ASP A   58  VAL A   72  1                                  15    
HELIX    4 AA4 PRO A   81  LYS A   86  1                                   6    
HELIX    5 AA5 GLY A   94  ALA A   98  5                                   5    
HELIX    6 AA6 SER A   99  ASN A  109  1                                  11    
SHEET    1 AA1 4 THR A  26  GLU A  28  0                                        
SHEET    2 AA1 4 VAL A   6  VAL A   9  1  N  VAL A   9   O  ILE A  27           
SHEET    3 AA1 4 VAL A  51  ILE A  53  1  O  ILE A  52   N  VAL A   8           
SHEET    4 AA1 4 LYS A  76  HIS A  77  1  O  LYS A  76   N  ILE A  53           
CRYST1   37.970   81.100   29.910  90.00  90.00  90.00 P 21 21 2     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      0.026337  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.012330  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.033434        0.00000