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Database: PDB
Entry: 4XJJ
LinkDB: 4XJJ
Original site: 4XJJ 
HEADER    CYTOKINE RECEPTOR                       08-JAN-15   4XJJ              
TITLE     EXTRACELLULAR DOMAIN OF TYPE II TRANSFORMING GROWTH FACTOR BETA       
TITLE    2 RECEPTOR IN COMPLEX WITH 2-(2-HYDROXYETHYL)NDSB-201                  
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: TGF-BETA RECEPTOR TYPE-2;                                  
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: LIGAND BINDING DOMAIN (UNP REISUDES 50-159);               
COMPND   5 SYNONYM: TGFR-2,TGF-BETA TYPE II RECEPTOR,TRANSFORMING GROWTH FACTOR-
COMPND   6 BETA RECEPTOR TYPE II,TBETAR-II;                                     
COMPND   7 EC: 2.7.11.30;                                                       
COMPND   8 ENGINEERED: YES;                                                     
COMPND   9 MUTATION: YES                                                        
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE   3 ORGANISM_COMMON: HUMAN;                                              
SOURCE   4 ORGANISM_TAXID: 9606;                                                
SOURCE   5 GENE: TGFBR2;                                                        
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 469008;                                     
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);                                 
SOURCE   9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;                              
SOURCE  10 EXPRESSION_SYSTEM_PLASMID: PET24A                                    
KEYWDS    TYPE II TRANSFORMING GROWTH FACTOR BETA RECEPTOR, NDSB-201,           
KEYWDS   2 TRANSFORMING GROWTH FACTOR BETA, KINASE, EXTRACELLULAR DOMAIN        
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    K.WANGKANONT,K.T.FOREST,L.L.KIESSLING                                 
REVDAT   1   24-JUN-15 4XJJ    0                                                
JRNL        AUTH   K.WANGKANONT,K.T.FOREST,L.L.KIESSLING                        
JRNL        TITL   EXTRACELLULAR DOMAIN OF TYPE II TRANSFORMING GROWTH FACTOR   
JRNL        TITL 2 BETA RECEPTOR IN COMPLEX WITH 2-(2-HYDROXYETHYL)NDSB-201     
JRNL        REF    TO BE PUBLISHED                                              
JRNL        REFN                                                                
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.40 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX                                               
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) : 1.40                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 27.74                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.360                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.5                           
REMARK   3   NUMBER OF REFLECTIONS             : 21988                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.155                           
REMARK   3   R VALUE            (WORKING SET) : 0.153                           
REMARK   3   FREE R VALUE                     : 0.185                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.000                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 1099                            
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 27.7420 -  2.7990    1.00     2781   146  0.1603 0.1720        
REMARK   3     2  2.7990 -  2.2219    1.00     2652   140  0.1771 0.2162        
REMARK   3     3  2.2219 -  1.9412    1.00     2628   138  0.1454 0.1937        
REMARK   3     4  1.9412 -  1.7637    1.00     2588   137  0.1354 0.1585        
REMARK   3     5  1.7637 -  1.6373    1.00     2618   138  0.1199 0.1943        
REMARK   3     6  1.6373 -  1.5408    1.00     2585   135  0.1251 0.1641        
REMARK   3     7  1.5408 -  1.4636    1.00     2559   135  0.1362 0.2035        
REMARK   3     8  1.4636 -  1.4000    0.96     2478   130  0.1631 0.1914        
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)     : 0.100            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.420           
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 13.14                          
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 21.10                          
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            943                                  
REMARK   3   ANGLE     :  1.091           1273                                  
REMARK   3   CHIRALITY :  0.047            137                                  
REMARK   3   PLANARITY :  0.004            168                                  
REMARK   3   DIHEDRAL  : 13.719            360                                  
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 4XJJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JAN-15.                  
REMARK 100 THE DEPOSITION ID IS D_1000205791.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 23-MAR-13                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 5.0                                
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-F                            
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.97872                            
REMARK 200  MONOCHROMATOR                  : C(111)                             
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CCD                                
REMARK 200  DETECTOR MANUFACTURER          : MARMOSAIC 225 MM CCD               
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : DENZO                              
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK                          
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 22047                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.400                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 30.400                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.8                               
REMARK 200  DATA REDUNDANCY                : 13.80                              
REMARK 200  R MERGE                    (I) : 0.06200                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 7.6000                             
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.45                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 97.6                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 11.80                              
REMARK 200  R MERGE FOR SHELL          (I) : 0.51900                            
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 2.5.6                                          
REMARK 200 STARTING MODEL: 1M9Z                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 45.55                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM CITRATE, 30% PEG 2000,     
REMARK 280  PH 5.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K             
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21                       
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X+1/2,-Y,Z+1/2                                         
REMARK 290       3555   -X,Y+1/2,-Z+1/2                                         
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       17.58500            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       38.17050            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       20.18650            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       38.17050            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       17.58500            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       20.18650            
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 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     MET A    25                                                      
REMARK 465     ASN A   131                                                      
REMARK 465     THR A   132                                                      
REMARK 465     SER A   133                                                      
REMARK 465     ASN A   134                                                      
REMARK 465     PRO A   135                                                      
REMARK 465     ASP A   136                                                      
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    ASP A  32     -143.33     53.36                                   
REMARK 500    PHE A 126       48.79   -100.32                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue 41D A 201                 
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 4P7U   RELATED DB: PDB                                   
DBREF  4XJJ A   27   136  UNP    P37173   TGFR2_HUMAN     50    159             
SEQADV 4XJJ MET A   25  UNP  P37173              EXPRESSION TAG                 
SEQADV 4XJJ ALA A   26  UNP  P37173              EXPRESSION TAG                 
SEQADV 4XJJ THR A   97  UNP  P37173    LYS   120 ENGINEERED MUTATION            
SEQRES   1 A  112  MET ALA LEU CYS LYS PHE CYS ASP VAL ARG PHE SER THR          
SEQRES   2 A  112  CYS ASP ASN GLN LYS SER CYS MET SER ASN CYS SER ILE          
SEQRES   3 A  112  THR SER ILE CYS GLU LYS PRO GLN GLU VAL CYS VAL ALA          
SEQRES   4 A  112  VAL TRP ARG LYS ASN ASP GLU ASN ILE THR LEU GLU THR          
SEQRES   5 A  112  VAL CYS HIS ASP PRO LYS LEU PRO TYR HIS ASP PHE ILE          
SEQRES   6 A  112  LEU GLU ASP ALA ALA SER PRO THR CYS ILE MET LYS GLU          
SEQRES   7 A  112  LYS LYS LYS PRO GLY GLU THR PHE PHE MET CYS SER CYS          
SEQRES   8 A  112  SER SER ASP GLU CYS ASN ASP ASN ILE ILE PHE SER GLU          
SEQRES   9 A  112  GLU TYR ASN THR SER ASN PRO ASP                              
HET    41D  A 201      16                                                       
HETNAM     41D 3-[2-(2-HYDROXYETHYL)PYRIDINIUM-1-YL]PROPANE-1-                  
HETNAM   2 41D  SULFONATE                                                       
FORMUL   2  41D    C10 H15 N O4 S                                               
FORMUL   3  HOH   *111(H2 O)                                                    
HELIX    1 AA1 GLU A  119  ASN A  121  5                                   3    
SHEET    1 AA1 2 LEU A  27  LYS A  29  0                                        
SHEET    2 AA1 2 THR A  51  ILE A  53 -1  O  SER A  52   N  CYS A  28           
SHEET    1 AA2 5 ASP A  32  PHE A  35  0                                        
SHEET    2 AA2 5 ILE A  72  HIS A  79 -1  O  LEU A  74   N  ARG A  34           
SHEET    3 AA2 5 VAL A  60  LYS A  67 -1  N  VAL A  60   O  HIS A  79           
SHEET    4 AA2 5 GLU A 108  CYS A 115 -1  O  PHE A 111   N  TRP A  65           
SHEET    5 AA2 5 LYS A 101  LYS A 105 -1  N  LYS A 103   O  PHE A 110           
SHEET    1 AA3 3 SER A  43  MET A  45  0                                        
SHEET    2 AA3 3 ASN A 123  ILE A 125 -1  O  ILE A 124   N  CYS A  44           
SHEET    3 AA3 3 CYS A  98  ILE A  99  1  N  CYS A  98   O  ILE A 125           
SSBOND   1 CYS A   28    CYS A   61                          1555   1555  2.03  
SSBOND   2 CYS A   31    CYS A   48                          1555   1555  2.04  
SSBOND   3 CYS A   38    CYS A   44                          1555   1555  2.03  
SSBOND   4 CYS A   54    CYS A   78                          1555   1555  2.05  
SSBOND   5 CYS A   98    CYS A  113                          1555   1555  2.05  
SSBOND   6 CYS A  115    CYS A  120                          1555   1555  2.05  
SITE     1 AC1  7 GLN A  41  TRP A  65  PHE A 111  PHE A 126                    
SITE     2 AC1  7 HOH A 317  HOH A 335  HOH A 393                               
CRYST1   35.170   40.373   76.341  90.00  90.00  90.00 P 21 21 21    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      0.028433  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.024769  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.013099        0.00000                         
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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