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Database: PDB
Entry: 5NOD
LinkDB: 5NOD
Original site: 5NOD 
HEADER    TRANSFERASE                             12-APR-17   5NOD              
TITLE     PASTA SUBUNIT 4 OF STREPTOCOCCUS PNEUMONIAE STKP CRYSTALLIZED WITH PEG
TITLE    2 AND SUCCINATE                                                        
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE STKP;                      
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: SER/THR-PROTEIN KINASE STKP,EUKARYOTIC-TYPE SER/THR PROTEIN 
COMPND   5 KINASE,ESTPK;                                                        
COMPND   6 EC: 2.7.11.1;                                                        
COMPND   7 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE (STRAIN ATCC BAA-255 / 
SOURCE   3 R6);                                                                 
SOURCE   4 ORGANISM_TAXID: 171101;                                              
SOURCE   5 GENE: STKP, PKN2, SPR1577;                                           
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562                                         
KEYWDS    PASTA, EXTRACELLULAR DOMAIN, SER/THR KINASE, STREPTOCOCCUS            
KEYWDS   2 PNEUMONIAE, TRANSFERASE                                              
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    F.GALISSON,V.GUEGUEN-CHAIGNON,P.GOUET,C.GRANGEASSE,L.ZUCCHINI         
REVDAT   4   12-JUN-19 5NOD    1       AUTHOR                                   
REVDAT   3   31-JAN-18 5NOD    1       JRNL                                     
REVDAT   2   13-DEC-17 5NOD    1       JRNL                                     
REVDAT   1   08-NOV-17 5NOD    0                                                
JRNL        AUTH   L.ZUCCHINI,C.MERCY,P.S.GARCIA,C.CLUZEL,V.GUEGUEN-CHAIGNON,   
JRNL        AUTH 2 F.GALISSON,C.FRETON,S.GUIRAL,C.BROCHIER-ARMANET,P.GOUET,     
JRNL        AUTH 3 C.GRANGEASSE                                                 
JRNL        TITL   PASTA REPEATS OF THE PROTEIN KINASE STKP INTERCONNECT CELL   
JRNL        TITL 2 CONSTRICTION AND SEPARATION OF STREPTOCOCCUS PNEUMONIAE.     
JRNL        REF    NAT MICROBIOL                 V.   3   197 2018              
JRNL        REFN                   ESSN 2058-5276                               
JRNL        PMID   29203882                                                     
JRNL        DOI    10.1038/S41564-017-0069-3                                    
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.90 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX 1.11.1_2575                                   
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) : 1.90                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 19.77                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.360                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 100.0                          
REMARK   3   NUMBER OF REFLECTIONS             : 7716                           
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.210                           
REMARK   3   R VALUE            (WORKING SET) : 0.209                           
REMARK   3   FREE R VALUE                     : 0.225                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 6.010                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 464                             
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 19.7748 -  2.7387    1.00     2521   161  0.2039 0.2033        
REMARK   3     2  2.7387 -  2.1747    1.00     2390   153  0.2271 0.2749        
REMARK   3     3  2.1747 -  1.9001    1.00     2341   150  0.2034 0.2502        
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)     : 0.130            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.750           
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 29.75                          
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 35.11                          
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : NULL                                                 
REMARK   3    B22 (A**2) : NULL                                                 
REMARK   3    B33 (A**2) : NULL                                                 
REMARK   3    B12 (A**2) : NULL                                                 
REMARK   3    B13 (A**2) : NULL                                                 
REMARK   3    B23 (A**2) : NULL                                                 
REMARK   3                                                                      
REMARK   3  TWINNING INFORMATION.                                               
REMARK   3   FRACTION: NULL                                                     
REMARK   3   OPERATOR: NULL                                                     
REMARK   3                                                                      
REMARK   3  DEVIATIONS FROM IDEAL VALUES.                                       
REMARK   3                 RMSD          COUNT                                  
REMARK   3   BOND      :  0.008            570                                  
REMARK   3   ANGLE     :  0.863            771                                  
REMARK   3   CHIRALITY :  0.057             96                                  
REMARK   3   PLANARITY :  0.004             97                                  
REMARK   3   DIHEDRAL  :  2.364            358                                  
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 5NOD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-APR-17.                  
REMARK 100 THE DEPOSITION ID IS D_1200003702.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 18-OCT-13                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 7.0                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : SLS                                
REMARK 200  BEAMLINE                       : X06DA                              
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.00003                            
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : PIXEL                              
REMARK 200  DETECTOR MANUFACTURER          : DECTRIS PILATUS 2M                 
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : XDS                                
REMARK 200  DATA SCALING SOFTWARE          : XSCALE                             
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 7718                               
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.900                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 19.774                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : -3.000                             
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.9                               
REMARK 200  DATA REDUNDANCY                : 12.38                              
REMARK 200  R MERGE                    (I) : 0.04200                            
REMARK 200  R SYM                      (I) : 0.04200                            
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 42.7000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.95                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 100.0                              
REMARK 200  DATA REDUNDANCY IN SHELL       : 11.77                              
REMARK 200  R MERGE FOR SHELL          (I) : 0.57700                            
REMARK 200  R SYM FOR SHELL            (I) : 0.57700                            
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 4.670                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: MOLREP                                                
REMARK 200 STARTING MODEL: 3OUV                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 50.92                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG3350 0,1M SUCCINATE PH 7.0,       
REMARK 280  VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K                     
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2                         
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -Y,X-Y,Z+2/3                                            
REMARK 290       3555   -X+Y,-X,Z+1/3                                           
REMARK 290       4555   -X,-Y,Z+1/2                                             
REMARK 290       5555   Y,-X+Y,Z+1/6                                            
REMARK 290       6555   X-Y,X,Z+5/6                                             
REMARK 290       7555   Y,X,-Z+2/3                                              
REMARK 290       8555   X-Y,-Y,-Z                                               
REMARK 290       9555   -X,-X+Y,-Z+1/3                                          
REMARK 290      10555   -Y,-X,-Z+1/6                                            
REMARK 290      11555   -X+Y,Y,-Z+1/2                                           
REMARK 290      12555   X,X-Y,-Z+5/6                                            
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 -0.500000 -0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   2  0.866025 -0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       27.30533            
REMARK 290   SMTRY1   3 -0.500000  0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   3 -0.866025 -0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       13.65267            
REMARK 290   SMTRY1   4 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000       20.47900            
REMARK 290   SMTRY1   5  0.500000  0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   5 -0.866025  0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   5  0.000000  0.000000  1.000000        6.82633            
REMARK 290   SMTRY1   6  0.500000 -0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   6  0.866025  0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   6  0.000000  0.000000  1.000000       34.13167            
REMARK 290   SMTRY1   7 -0.500000  0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   7  0.866025  0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   7  0.000000  0.000000 -1.000000       27.30533            
REMARK 290   SMTRY1   8  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   8  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   8  0.000000  0.000000 -1.000000        0.00000            
REMARK 290   SMTRY1   9 -0.500000 -0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   9 -0.866025  0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   9  0.000000  0.000000 -1.000000       13.65267            
REMARK 290   SMTRY1  10  0.500000 -0.866025  0.000000        0.00000            
REMARK 290   SMTRY2  10 -0.866025 -0.500000  0.000000        0.00000            
REMARK 290   SMTRY3  10  0.000000  0.000000 -1.000000        6.82633            
REMARK 290   SMTRY1  11 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2  11  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3  11  0.000000  0.000000 -1.000000       20.47900            
REMARK 290   SMTRY1  12  0.500000  0.866025  0.000000        0.00000            
REMARK 290   SMTRY2  12  0.866025 -0.500000  0.000000        0.00000            
REMARK 290   SMTRY3  12  0.000000  0.000000 -1.000000       34.13167            
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: 4840 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            
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   575                                                      
REMARK 465     HIS A   576                                                      
REMARK 465     MET A   577                                                      
REMARK 465     LYS A   578                                                      
REMARK 465     THR A   654                                                      
REMARK 465     THR A   655                                                      
REMARK 465     SER A   656                                                      
REMARK 465     ALA A   657                                                      
REMARK 465     THR A   658                                                      
REMARK 465     PRO A   659                                                      
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    THR A 580       70.62   -103.20                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
DBREF  5NOD A  578   659  UNP    Q8DNS0   STKP_STRR6     578    659             
SEQADV 5NOD GLY A  575  UNP  Q8DNS0              EXPRESSION TAG                 
SEQADV 5NOD HIS A  576  UNP  Q8DNS0              EXPRESSION TAG                 
SEQADV 5NOD MET A  577  UNP  Q8DNS0              EXPRESSION TAG                 
SEQRES   1 A   85  GLY HIS MET LYS VAL THR SER VAL ALA MET PRO SER TYR          
SEQRES   2 A   85  ILE GLY SER SER LEU GLU PHE THR LYS ASN ASN LEU ILE          
SEQRES   3 A   85  GLN ILE VAL GLY ILE LYS GLU ALA ASN ILE GLU VAL VAL          
SEQRES   4 A   85  GLU VAL THR THR ALA PRO ALA GLY SER VAL GLU GLY MET          
SEQRES   5 A   85  VAL VAL GLU GLN SER PRO ARG ALA GLY GLU LYS VAL ASP          
SEQRES   6 A   85  LEU ASN LYS THR ARG VAL LYS ILE SER ILE TYR LYS PRO          
SEQRES   7 A   85  LYS THR THR SER ALA THR PRO                                  
FORMUL   2  HOH   *38(H2 O)                                                     
HELIX    1 AA1 SER A  591  ILE A  602  1                                  12    
HELIX    2 AA2 LYS A  606  ALA A  608  5                                   3    
SHEET    1 AA1 2 SER A 581  ALA A 583  0                                        
SHEET    2 AA1 2 LYS A 637  ASP A 639 -1  O  VAL A 638   N  VAL A 582           
SHEET    1 AA2 3 ILE A 610  VAL A 615  0                                        
SHEET    2 AA2 3 VAL A 645  TYR A 650  1  O  ILE A 649   N  VAL A 615           
SHEET    3 AA2 3 VAL A 627  SER A 631 -1  N  GLU A 629   O  SER A 648           
CISPEP   1 SER A  631    PRO A  632          0        -1.63                     
CRYST1   87.760   87.760   40.958  90.00  90.00 120.00 P 65 2 2     12          
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      0.011395  0.006579  0.000000        0.00000                         
SCALE2      0.000000  0.013157  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.024415        0.00000                         
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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