PDB Short entry for 5WWW
HEADER    RNA BINDING PROTEIN/RNA                 05-JAN-17   5WWW              
TITLE     CRYSTAL STRUCTURE OF THE KH1 DOMAIN OF HUMAN RNA-BINDING E3 UBIQUITIN-
TITLE    2 PROTEIN LIGASE MEX-3C COMPLEX WITH RNA                               
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: RNA-BINDING E3 UBIQUITIN-PROTEIN LIGASE MEX3C;             
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: KH1 DOMAIN, UNP RESIDUES 221-306;                          
COMPND   5 SYNONYM: RING FINGER AND KH DOMAIN-CONTAINING PROTEIN 2,RING FINGER  
COMPND   6 PROTEIN 194,RING-TYPE E3 UBIQUITIN TRANSFERASE MEX3C;                
COMPND   7 EC: 2.3.2.27;                                                        
COMPND   8 ENGINEERED: YES;                                                     
COMPND   9 MOL_ID: 2;                                                           
COMPND  10 MOLECULE: RNA (5'-R(*GP*UP*UP*UP*AP*G)-3');                          
COMPND  11 CHAIN: B;                                                            
COMPND  12 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: MEX3C, RKHD2, RNF194, BM-013;                                  
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE   8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;                              
SOURCE   9 MOL_ID: 2;                                                           
SOURCE  10 SYNTHETIC: YES;                                                      
SOURCE  11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;                            
SOURCE  12 ORGANISM_TAXID: 32630                                                
KEYWDS    KH1, MEX-3C, RNA, RNA BINDING PROTEIN-RNA COMPLEX                     
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    L.YANG,C.WANG,F.LI,Q.GONG                                             
REVDAT   2   11-OCT-17 5WWW    1       JRNL                                     
REVDAT   1   23-AUG-17 5WWW    0                                                
JRNL        AUTH   L.YANG,C.WANG,F.LI,J.ZHANG,A.NAYAB,J.WU,Y.SHI,Q.GONG         
JRNL        TITL   THE HUMAN RNA-BINDING PROTEIN AND E3 LIGASE MEX-3C BINDS THE 
JRNL        TITL 2 MEX-3-RECOGNITION ELEMENT (MRE) MOTIF WITH HIGH AFFINITY     
JRNL        REF    J. BIOL. CHEM.                V. 292 16221 2017              
JRNL        REFN                   ESSN 1083-351X                               
JRNL        PMID   28808060                                                     
JRNL        DOI    10.1074/JBC.M117.797746                                      
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.80 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX 1.10_2155                                     
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) : 1.80                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 38.18                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.410                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.5                           
REMARK   3   NUMBER OF REFLECTIONS             : 11402                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.174                           
REMARK   3   R VALUE            (WORKING SET) : 0.172                           
REMARK   3   FREE R VALUE                     : 0.209                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 4.950                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 564                             
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 38.1916 -  2.8538    1.00     2776   143  0.1634 0.1925        
REMARK   3     2  2.8538 -  2.2652    1.00     2714   138  0.1815 0.2161        
REMARK   3     3  2.2652 -  1.9789    1.00     2687   149  0.1737 0.2359        
REMARK   3     4  1.9789 -  1.7979    0.99     2661   134  0.1935 0.2392        
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) : 22.370           
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 22.96                          
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 26.33                          
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            917                                  
REMARK   3   ANGLE     :  0.778           1270                                  
REMARK   3   CHIRALITY :  0.049            148                                  
REMARK   3   PLANARITY :  0.007            144                                  
REMARK   3   DIHEDRAL  : 15.672            562                                  
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 5WWW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JAN-17.                  
REMARK 100 THE DEPOSITION ID IS D_1300002529.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 12-DEC-15                          
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               : SSRF                               
REMARK 200  BEAMLINE                       : BL18U1                             
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.979                              
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 : MOSFLM                             
REMARK 200  DATA SCALING SOFTWARE          : HKL-2000, HKL-2000, HKL            
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 11406                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.800                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 40.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.6                               
REMARK 200  DATA REDUNDANCY                : 10.10                              
REMARK 200  R MERGE                    (I) : 0.15900                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 3.6000                             
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.86                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 98.9                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 10.30                              
REMARK 200  R MERGE FOR SHELL          (I) : 0.70500                            
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: 2DGR                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 50.19                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 5% V/V TACSIMATE PH 7.0, 0.1M HEPES PH   
REMARK 280  7.0, 10% W/V POLYETHYLENE GLYCOL MONOMETHYL ETHER 2000, VAPOR       
REMARK 280  DIFFUSION, HANGING DROP, TEMPERATURE 293K                           
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62                             
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                                                 
REMARK 290       5555   Y,-X+Y,Z+2/3                                            
REMARK 290       6555   X-Y,X,Z+1/3                                             
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       24.26133            
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       12.13067            
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        0.00000            
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       24.26133            
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       12.13067            
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: 1490 ANGSTROM**2                          
REMARK 350 SURFACE AREA OF THE COMPLEX: 6970 ANGSTROM**2                        
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL                         
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B                                  
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 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 401  LIES ON A SPECIAL POSITION.                          
REMARK 375      HOH A 466  LIES ON A SPECIAL POSITION.                          
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    LYS A 228      -82.27   -103.16                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
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 476        DISTANCE =  7.88 ANGSTROMS                       
REMARK 525    HOH A 477        DISTANCE =  8.03 ANGSTROMS                       
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 5WWX   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 5WWZ   RELATED DB: PDB                                   
DBREF  5WWW A  221   306  UNP    Q5U5Q3   MEX3C_HUMAN    221    306             
DBREF  5WWW B    4     9  PDB    5WWW     5WWW             4      9             
SEQADV 5WWW GLY A  213  UNP  Q5U5Q3              EXPRESSION TAG                 
SEQADV 5WWW HIS A  214  UNP  Q5U5Q3              EXPRESSION TAG                 
SEQADV 5WWW HIS A  215  UNP  Q5U5Q3              EXPRESSION TAG                 
SEQADV 5WWW HIS A  216  UNP  Q5U5Q3              EXPRESSION TAG                 
SEQADV 5WWW HIS A  217  UNP  Q5U5Q3              EXPRESSION TAG                 
SEQADV 5WWW HIS A  218  UNP  Q5U5Q3              EXPRESSION TAG                 
SEQADV 5WWW HIS A  219  UNP  Q5U5Q3              EXPRESSION TAG                 
SEQADV 5WWW MET A  220  UNP  Q5U5Q3              EXPRESSION TAG                 
SEQRES   1 A   94  GLY HIS HIS HIS HIS HIS HIS MET GLN ALA ALA LEU LEU          
SEQRES   2 A   94  ARG ARG LYS SER VAL ASN THR THR GLU CYS VAL PRO VAL          
SEQRES   3 A   94  PRO SER SER GLU HIS VAL ALA GLU ILE VAL GLY ARG GLN          
SEQRES   4 A   94  GLY CYS LYS ILE LYS ALA LEU ARG ALA LYS THR ASN THR          
SEQRES   5 A   94  TYR ILE LYS THR PRO VAL ARG GLY GLU GLU PRO ILE PHE          
SEQRES   6 A   94  VAL VAL THR GLY ARG LYS GLU ASP VAL ALA MET ALA LYS          
SEQRES   7 A   94  ARG GLU ILE LEU SER ALA ALA GLU HIS PHE SER MET ILE          
SEQRES   8 A   94  ARG ALA SER                                                  
SEQRES   1 B    6    G   U   U   U   A   G                                      
FORMUL   3  HOH   *93(H2 O)                                                     
HELIX    1 AA1 GLY A  213  ARG A  227  1                                  15    
HELIX    2 AA2 SER A  240  GLY A  249  1                                  10    
HELIX    3 AA3 GLY A  252  ASN A  263  1                                  12    
HELIX    4 AA4 ARG A  282  ALA A  305  1                                  24    
SHEET    1 AA1 3 THR A 232  PRO A 237  0                                        
SHEET    2 AA1 3 ILE A 276  GLY A 281 -1  O  PHE A 277   N  VAL A 236           
SHEET    3 AA1 3 TYR A 265  LYS A 267 -1  N  LYS A 267   O  VAL A 278           
CRYST1   76.366   76.366   36.392  90.00  90.00 120.00 P 62          6          
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      0.013095  0.007560  0.000000        0.00000                         
SCALE2      0.000000  0.015121  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.027479        0.00000