PDB Short entry for 5TO5
HEADER    CELL CYCLE                              16-OCT-16   5TO5              
TITLE     STRUCTURE OF THE TPR OLIGOMERIZATION DOMAIN                           
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: NUCLEOPROTEIN TPR;                                         
COMPND   3 CHAIN: A, B;                                                         
COMPND   4 FRAGMENT: UNP RESIDUES 2-142;                                        
COMPND   5 SYNONYM: MEGATOR,NPC-ASSOCIATED INTRANUCLEAR PROTEIN,TRANSLOCATED    
COMPND   6 PROMOTER REGION PROTEIN;                                             
COMPND   7 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: TPR;                                                           
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);                       
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 469008                                      
KEYWDS    TPR OLIGOMERIZATION DOMAIN, RECEPTOR TYROSINE KINASE, MET, ONCOGENIC  
KEYWDS   2 FUSION KINASES, CELL CYCLE                                           
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    K.PAL,Q.XU,X.E.ZHOU,K.MELCHER,H.E.XU                                  
REVDAT   2   01-MAY-19 5TO5    1       JRNL                                     
REVDAT   1   18-OCT-17 5TO5    0                                                
JRNL        AUTH   K.PAL,A.BANDYOPADHYAY,X.E.ZHOU,Q.XU,D.P.MARCIANO,            
JRNL        AUTH 2 J.S.BRUNZELLE,S.YERRUM,P.R.GRIFFIN,G.VANDE WOUDE,K.MELCHER,  
JRNL        AUTH 3 H.E.XU                                                       
JRNL        TITL   STRUCTURAL BASIS OF TPR-MEDIATED OLIGOMERIZATION AND         
JRNL        TITL 2 ACTIVATION OF ONCOGENIC FUSION KINASES.                      
JRNL        REF    STRUCTURE                     V.  25   867 2017              
JRNL        REFN                   ISSN 0969-2126                               
JRNL        PMID   28528776                                                     
JRNL        DOI    10.1016/J.STR.2017.04.015                                    
REMARK   2                                                                      
REMARK   2 RESOLUTION.    2.50 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX 1.9_1692                                      
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) : 2.50                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 21.41                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.940                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 95.9                           
REMARK   3   NUMBER OF REFLECTIONS             : 11481                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.232                           
REMARK   3   R VALUE            (WORKING SET) : 0.229                           
REMARK   3   FREE R VALUE                     : 0.282                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 4.740                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 544                             
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 21.4123 -  3.9623    0.92     2670   129  0.2020 0.2572        
REMARK   3     2  3.9623 -  3.1482    0.96     2734   138  0.2273 0.2731        
REMARK   3     3  3.1482 -  2.7512    0.98     2790   137  0.2543 0.2981        
REMARK   3     4  2.7512 -  2.5001    0.98     2743   140  0.2722 0.3450        
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELLING.                                             
REMARK   3   METHOD USED        : NULL                                          
REMARK   3   SOLVENT RADIUS     : 1.10                                          
REMARK   3   SHRINKAGE RADIUS   : 1.00                                          
REMARK   3   K_SOL              : NULL                                          
REMARK   3   B_SOL              : NULL                                          
REMARK   3                                                                      
REMARK   3  ERROR ESTIMATES.                                                    
REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.350            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.960           
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 37.55                          
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      :  0.004           2349                                  
REMARK   3   ANGLE     :  0.722           3135                                  
REMARK   3   CHIRALITY :  0.026            355                                  
REMARK   3   PLANARITY :  0.003            415                                  
REMARK   3   DIHEDRAL  : 17.522            973                                  
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 5TO5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-OCT-16.                  
REMARK 100 THE DEPOSITION ID IS D_1000223447.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 16-MAR-13                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 6.25                               
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : APS                                
REMARK 200  BEAMLINE                       : 21-ID-D                            
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.07812                            
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CCD                                
REMARK 200  DETECTOR MANUFACTURER          : RAYONIX MX300-HS                   
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000                           
REMARK 200  DATA SCALING SOFTWARE          : HKL-2000                           
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 17251                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.180                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 21.850                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 96.0                               
REMARK 200  DATA REDUNDANCY                : 5.700                              
REMARK 200  R MERGE                    (I) : 0.07900                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 15.8000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : NULL                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : NULL                               
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : NULL                               
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: MOLREP                                                
REMARK 200 STARTING MODEL: NULL                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 52.07                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG1.5K, 0.1M BISTRIS (6.25), PH     
REMARK 280  6.25, EVAPORATION, TEMPERATURE 295K                                 
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1                          
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X,Y,-Z                                                 
REMARK 290       3555   X+1/2,Y+1/2,Z                                           
REMARK 290       4555   -X+1/2,Y+1/2,-Z                                         
REMARK 290                                                                      
REMARK 290     WHERE NNN -> OPERATOR NUMBER                                     
REMARK 290           MMM -> TRANSLATION VECTOR                                  
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                            
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM             
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY                
REMARK 290 RELATED MOLECULES.                                                   
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   2  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000 -1.000000        0.00000            
REMARK 290   SMTRY1   3  1.000000  0.000000  0.000000       37.08850            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       25.77550            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   4 -1.000000  0.000000  0.000000       37.08850            
REMARK 290   SMTRY2   4  0.000000  1.000000  0.000000       25.77550            
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000            
REMARK 290                                                                      
REMARK 290 REMARK: NULL                                                         
REMARK 300                                                                      
REMARK 300 BIOMOLECULE: 1                                                       
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM                
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN                  
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON               
REMARK 300 BURIED SURFACE AREA.                                                 
REMARK 350                                                                      
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN           
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE                
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS          
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND                          
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.                               
REMARK 350                                                                      
REMARK 350 BIOMOLECULE: 1                                                       
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC                           
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC                    
REMARK 350 SOFTWARE USED: PISA                                                  
REMARK 350 TOTAL BURIED SURFACE AREA: 7110 ANGSTROM**2                          
REMARK 350 SURFACE AREA OF THE COMPLEX: 20160 ANGSTROM**2                       
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 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 B 263  LIES ON A SPECIAL POSITION.                          
REMARK 465                                                                      
REMARK 465 MISSING RESIDUES                                                     
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE                       
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)                
REMARK 465                                                                      
REMARK 465   M RES C SSSEQI                                                     
REMARK 465     ALA B     2                                                      
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES                                       
REMARK 500                                                                      
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES              
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE               
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                 
REMARK 500                                                                      
REMARK 500 STANDARD TABLE:                                                      
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)              
REMARK 500                                                                      
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999                        
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996                     
REMARK 500                                                                      
REMARK 500  M RES CSSEQI ATM1   ATM2   ATM3                                     
REMARK 500    LEU B  80   CB  -  CG  -  CD1 ANGL. DEV. = -17.7 DEGREES          
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 263        DISTANCE =  6.12 ANGSTROMS                       
REMARK 525    HOH B 263        DISTANCE =  6.07 ANGSTROMS                       
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 5TO6   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 5TO7   RELATED DB: PDB                                   
DBREF  5TO5 A    2   142  UNP    P12270   TPR_HUMAN        2    142             
DBREF  5TO5 B    2   142  UNP    P12270   TPR_HUMAN        2    142             
SEQADV 5TO5 MET A   55  UNP  P12270    PHE    55 ENGINEERED MUTATION            
SEQADV 5TO5 MET A  113  UNP  P12270    PHE   113 ENGINEERED MUTATION            
SEQADV 5TO5 MET B   55  UNP  P12270    PHE    55 ENGINEERED MUTATION            
SEQADV 5TO5 MET B  113  UNP  P12270    PHE   113 ENGINEERED MUTATION            
SEQRES   1 A  141  ALA ALA VAL LEU GLN GLN VAL LEU GLU ARG THR GLU LEU          
SEQRES   2 A  141  ASN LYS LEU PRO LYS SER VAL GLN ASN LYS LEU GLU LYS          
SEQRES   3 A  141  PHE LEU ALA ASP GLN GLN SER GLU ILE ASP GLY LEU LYS          
SEQRES   4 A  141  GLY ARG HIS GLU LYS PHE LYS VAL GLU SER GLU GLN GLN          
SEQRES   5 A  141  TYR MET GLU ILE GLU LYS ARG LEU SER HIS SER GLN GLU          
SEQRES   6 A  141  ARG LEU VAL ASN GLU THR ARG GLU CYS GLN SER LEU ARG          
SEQRES   7 A  141  LEU GLU LEU GLU LYS LEU ASN ASN GLN LEU LYS ALA LEU          
SEQRES   8 A  141  THR GLU LYS ASN LYS GLU LEU GLU ILE ALA GLN ASP ARG          
SEQRES   9 A  141  ASN ILE ALA ILE GLN SER GLN MET THR ARG THR LYS GLU          
SEQRES  10 A  141  GLU LEU GLU ALA GLU LYS ARG ASP LEU ILE ARG THR ASN          
SEQRES  11 A  141  GLU ARG LEU SER GLN GLU LEU GLU TYR LEU THR                  
SEQRES   1 B  141  ALA ALA VAL LEU GLN GLN VAL LEU GLU ARG THR GLU LEU          
SEQRES   2 B  141  ASN LYS LEU PRO LYS SER VAL GLN ASN LYS LEU GLU LYS          
SEQRES   3 B  141  PHE LEU ALA ASP GLN GLN SER GLU ILE ASP GLY LEU LYS          
SEQRES   4 B  141  GLY ARG HIS GLU LYS PHE LYS VAL GLU SER GLU GLN GLN          
SEQRES   5 B  141  TYR MET GLU ILE GLU LYS ARG LEU SER HIS SER GLN GLU          
SEQRES   6 B  141  ARG LEU VAL ASN GLU THR ARG GLU CYS GLN SER LEU ARG          
SEQRES   7 B  141  LEU GLU LEU GLU LYS LEU ASN ASN GLN LEU LYS ALA LEU          
SEQRES   8 B  141  THR GLU LYS ASN LYS GLU LEU GLU ILE ALA GLN ASP ARG          
SEQRES   9 B  141  ASN ILE ALA ILE GLN SER GLN MET THR ARG THR LYS GLU          
SEQRES  10 B  141  GLU LEU GLU ALA GLU LYS ARG ASP LEU ILE ARG THR ASN          
SEQRES  11 B  141  GLU ARG LEU SER GLN GLU LEU GLU TYR LEU THR                  
FORMUL   3  HOH   *126(H2 O)                                                    
HELIX    1 AA1 VAL A    4  LEU A    9  1                                   6    
HELIX    2 AA2 GLU A   10  ASN A   15  1                                   6    
HELIX    3 AA3 PRO A   18  LEU A  141  1                                 124    
HELIX    4 AA4 VAL B    4  LEU B    9  1                                   6    
HELIX    5 AA5 GLU B   10  ASN B   15  1                                   6    
HELIX    6 AA6 PRO B   18  THR B  142  1                                 125    
CRYST1   74.177   51.551   94.980  90.00 107.83  90.00 C 1 2 1       8          
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      0.013481  0.000000  0.004337        0.00000                         
SCALE2      0.000000  0.019398  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.011060        0.00000