PDB Short entry for 2JM1
HEADER    METAL BINDING PROTEIN                   13-SEP-06   2JM1              
TITLE     STRUCTURES AND CHEMICAL SHIFT ASSIGNMENTS FOR THE ADD DOMAIN OF THE   
TITLE    2 ATRX PROTEIN                                                         
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: TRANSCRIPTIONAL REGULATOR ATRX;                            
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: ADD DOMAIN, RESIDUES 159-296;                              
COMPND   5 SYNONYM: ATP-DEPENDENT HELICASE ATRX, X-LINKED HELICASE II, X-LINKED 
COMPND   6 NUCLEAR PROTEIN, XNP, ZNF- HX;                                       
COMPND   7 EC: 3.6.1.-;                                                         
COMPND   8 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: ATRX, RAD54L, XH2;                                             
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: BL21 DE3 ROSETTA PLYSS;                    
SOURCE   9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;                              
SOURCE  10 EXPRESSION_SYSTEM_PLASMID: PET30A                                    
KEYWDS    ADD DOMAIN, METAL BINDING PROTEIN                                     
EXPDTA    SOLUTION NMR                                                          
NUMMDL    32                                                                    
AUTHOR    J.YANG,D.NEUHAUS                                                      
REVDAT   3   23-JUN-10 2JM1    1       JRNL                                     
REVDAT   2   24-FEB-09 2JM1    1       VERSN                                    
REVDAT   1   26-JUN-07 2JM1    0                                                
JRNL        AUTH   A.ARGENTARO,J.C.YANG,L.CHAPMAN,M.S.KOWALCZYK,R.J.GIBBONS,    
JRNL        AUTH 2 D.R.HIGGS,D.NEUHAUS,D.RHODES                                 
JRNL        TITL   STRUCTURAL CONSEQUENCES OF DISEASE-CAUSING MUTATIONS IN THE  
JRNL        TITL 2 ATRX-DNMT3-DNMT3L (ADD) DOMAIN OF THE CHROMATIN-ASSOCIATED   
JRNL        TITL 3 PROTEIN ATRX.                                                
JRNL        REF    PROC.NATL.ACAD.SCI.USA        V. 104 11939 2007              
JRNL        REFN                   ISSN 0027-8424                               
JRNL        PMID   17609377                                                     
JRNL        DOI    10.1073/PNAS.0704057104                                      
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : X-PLOR 3.8                                           
REMARK   3   AUTHORS     : AT BRUNGER                                           
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 2JM1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-SEP-06.                  
REMARK 100 THE RCSB ID CODE IS RCSB100001.                                      
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 300                                
REMARK 210  PH                             : 6.7                                
REMARK 210  IONIC STRENGTH                 : 0.5                                
REMARK 210  PRESSURE                       : AMBIENT                            
REMARK 210  SAMPLE CONTENTS                : 0.7 MM [U-15N] ADD DOMAIN 156-     
REMARK 210                                   296, 20 MM TRIS, 1 MM DTT, 100 UM  
REMARK 210                                   ZINC CHLORIDE, 0.5 M SODIUM        
REMARK 210                                   CHLORIDE, 93% H2O, 7% D2O; 0.35    
REMARK 210                                   MM [U-13C; U-15N] ADD DOMAIN 156-  
REMARK 210                                   296, 20 MM TRIS, 1 MM DTT, 100 UM  
REMARK 210                                   ZINC CHLORIDE, 0.5 M SODIUM        
REMARK 210                                   CHLORIDE, 93% H2O, 7% D2O          
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 2D 1H-15N HSQC; 2D NOESY; 3D 1H-   
REMARK 210                                   15N NOESY; 3D HNHB; 2D 1H-13C      
REMARK 210                                   HSQC; 3D HNCACB; 3D HN(CO)CACB;    
REMARK 210                                   HNHAHB; HN(CO)HAHB; 3D HCCH-       
REMARK 210                                   TOCSY; 3D HCCH-COSY; 3D 1H-13C     
REMARK 210                                   NOESY                              
REMARK 210  SPECTROMETER FIELD STRENGTH    : 800 MHZ; 500 MHZ                   
REMARK 210  SPECTROMETER MODEL             : AVANCE; DRX                        
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : XWINNMR 3.5, SPARKY, X-PLOR 3.8    
REMARK 210   METHOD USED                   : SIMULATED ANNEALING                
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 100                                
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 32                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : LOWEST ENERGY                      
REMARK 210                                                                      
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1                   
REMARK 210                                                                      
REMARK 210 REMARK: NULL                                                         
REMARK 215                                                                      
REMARK 215 NMR STUDY                                                            
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION           
REMARK 215 NMR DATA.  PROTEIN DATA BANK CONVENTIONS REQUIRE THAT                
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON              
REMARK 215 THESE RECORDS ARE MEANINGLESS.                                       
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  1 ASN A 179       95.06    -51.13                                   
REMARK 500  1 HIS A 180     -175.58     51.31                                   
REMARK 500  1 SER A 185      -69.07    -94.93                                   
REMARK 500  1 ILE A 186      157.27    -49.66                                   
REMARK 500  1 SER A 210      110.89   -169.15                                   
REMARK 500  1 ARG A 211       81.19     51.55                                   
REMARK 500  1 SER A 213      -71.15     64.33                                   
REMARK 500  1 GLU A 218       51.74   -144.09                                   
REMARK 500  1 TRP A 222      -59.95   -149.84                                   
REMARK 500  1 GLU A 225     -169.77   -123.55                                   
REMARK 500  1 ASN A 228       91.95     52.06                                   
REMARK 500  1 PHE A 234      -60.11   -147.67                                   
REMARK 500  1 LEU A 248       26.58   -148.35                                   
REMARK 500  1 ASP A 258       69.54   -170.04                                   
REMARK 500  1 GLU A 259      -67.28   -131.62                                   
REMARK 500  1 ASN A 260       40.75   -146.29                                   
REMARK 500  1 GLN A 262      111.84   -170.71                                   
REMARK 500  1 CYS A 265     -147.36   -141.72                                   
REMARK 500  1 LEU A 273       31.55   -147.93                                   
REMARK 500  2 MET A 158      -60.04   -142.40                                   
REMARK 500  2 LEU A 165       87.94     52.81                                   
REMARK 500  2 ASN A 179       93.78    -52.63                                   
REMARK 500  2 HIS A 180     -174.74     50.71                                   
REMARK 500  2 SER A 185      -69.35    -93.23                                   
REMARK 500  2 SER A 210     -167.49   -112.45                                   
REMARK 500  2 ASP A 212      178.55    -53.40                                   
REMARK 500  2 ASP A 214       30.90    -98.47                                   
REMARK 500  2 TRP A 222      -60.39   -149.94                                   
REMARK 500  2 ASP A 233       40.57   -107.30                                   
REMARK 500  2 PHE A 234      -58.67   -151.03                                   
REMARK 500  2 LEU A 248       25.02   -145.93                                   
REMARK 500  2 ASP A 258       61.06   -170.86                                   
REMARK 500  2 GLU A 259      -65.69   -128.59                                   
REMARK 500  2 ASN A 260       36.13   -152.33                                   
REMARK 500  2 CYS A 265     -148.52   -123.26                                   
REMARK 500  2 PRO A 270       74.03    -68.65                                   
REMARK 500  2 LEU A 273       35.09   -155.60                                   
REMARK 500  2 GLN A 293       46.91   -101.68                                   
REMARK 500  2 ASN A 294       82.70   -153.47                                   
REMARK 500  3 ASN A 179       94.03    -52.94                                   
REMARK 500  3 HIS A 180     -173.84     51.45                                   
REMARK 500  3 SER A 185      -69.12    -92.58                                   
REMARK 500  3 SER A 210      108.98   -170.37                                   
REMARK 500  3 ARG A 211       77.56     52.48                                   
REMARK 500  3 SER A 213      -74.73     61.24                                   
REMARK 500  3 GLU A 218       52.78   -145.97                                   
REMARK 500  3 TRP A 222      -60.59   -149.79                                   
REMARK 500  3 GLU A 225     -169.01   -117.81                                   
REMARK 500  3 PHE A 234      -60.79   -150.06                                   
REMARK 500  3 LEU A 248       24.59   -145.32                                   
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS     611 RAMACHANDRAN OUTLIERS.                        
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: PLANAR GROUPS                                              
REMARK 500                                                                      
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL                 
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE                    
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN                    
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS                        
REMARK 500 AN RMSD GREATER THAN THIS VALUE                                      
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                             
REMARK 500                                                                      
REMARK 500  M RES CSSEQI        RMS     TYPE                                    
REMARK 500  1 ARG A 160         0.24    SIDE CHAIN                              
REMARK 500  1 ARG A 188         0.28    SIDE CHAIN                              
REMARK 500  1 ARG A 211         0.31    SIDE CHAIN                              
REMARK 500  1 ARG A 221         0.27    SIDE CHAIN                              
REMARK 500  1 ARG A 246         0.30    SIDE CHAIN                              
REMARK 500  1 ARG A 250         0.32    SIDE CHAIN                              
REMARK 500  2 ARG A 160         0.31    SIDE CHAIN                              
REMARK 500  2 ARG A 188         0.32    SIDE CHAIN                              
REMARK 500  2 ARG A 211         0.26    SIDE CHAIN                              
REMARK 500  2 ARG A 221         0.22    SIDE CHAIN                              
REMARK 500  2 ARG A 246         0.31    SIDE CHAIN                              
REMARK 500  2 ARG A 250         0.32    SIDE CHAIN                              
REMARK 500  3 ARG A 160         0.26    SIDE CHAIN                              
REMARK 500  3 ARG A 188         0.26    SIDE CHAIN                              
REMARK 500  3 ARG A 211         0.29    SIDE CHAIN                              
REMARK 500  3 ARG A 221         0.21    SIDE CHAIN                              
REMARK 500  3 ARG A 246         0.28    SIDE CHAIN                              
REMARK 500  3 ARG A 250         0.30    SIDE CHAIN                              
REMARK 500  4 ARG A 160         0.24    SIDE CHAIN                              
REMARK 500  4 ARG A 188         0.31    SIDE CHAIN                              
REMARK 500  4 ARG A 211         0.27    SIDE CHAIN                              
REMARK 500  4 ARG A 221         0.30    SIDE CHAIN                              
REMARK 500  4 ARG A 246         0.29    SIDE CHAIN                              
REMARK 500  4 ARG A 250         0.30    SIDE CHAIN                              
REMARK 500  5 ARG A 160         0.28    SIDE CHAIN                              
REMARK 500  5 ARG A 188         0.24    SIDE CHAIN                              
REMARK 500  5 ARG A 211         0.21    SIDE CHAIN                              
REMARK 500  5 ARG A 221         0.29    SIDE CHAIN                              
REMARK 500  5 ARG A 246         0.30    SIDE CHAIN                              
REMARK 500  5 ARG A 250         0.21    SIDE CHAIN                              
REMARK 500  6 ARG A 160         0.32    SIDE CHAIN                              
REMARK 500  6 ARG A 188         0.24    SIDE CHAIN                              
REMARK 500  6 ARG A 211         0.23    SIDE CHAIN                              
REMARK 500  6 ARG A 221         0.27    SIDE CHAIN                              
REMARK 500  6 ARG A 246         0.24    SIDE CHAIN                              
REMARK 500  6 ARG A 250         0.27    SIDE CHAIN                              
REMARK 500  7 ARG A 160         0.32    SIDE CHAIN                              
REMARK 500  7 ARG A 188         0.22    SIDE CHAIN                              
REMARK 500  7 ARG A 211         0.28    SIDE CHAIN                              
REMARK 500  7 ARG A 221         0.31    SIDE CHAIN                              
REMARK 500  7 ARG A 246         0.30    SIDE CHAIN                              
REMARK 500  7 ARG A 250         0.31    SIDE CHAIN                              
REMARK 500  8 ARG A 160         0.25    SIDE CHAIN                              
REMARK 500  8 ARG A 188         0.28    SIDE CHAIN                              
REMARK 500  8 ARG A 211         0.26    SIDE CHAIN                              
REMARK 500  8 ARG A 221         0.29    SIDE CHAIN                              
REMARK 500  8 ARG A 246         0.32    SIDE CHAIN                              
REMARK 500  8 ARG A 250         0.24    SIDE CHAIN                              
REMARK 500  9 ARG A 160         0.32    SIDE CHAIN                              
REMARK 500  9 ARG A 188         0.31    SIDE CHAIN                              
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS     192 PLANE DEVIATIONS.                             
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 620                                                                      
REMARK 620 METAL COORDINATION                                                   
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):                             
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                           1  ZN A   1  ZN                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 CYS A 171   SG                                                     
REMARK 620 2 CYS A 174   SG  112.6                                              
REMARK 620 3 CYS A 197   SG  111.6 110.2                                        
REMARK 620 4 CYS A 200   SG  110.0 103.2 108.8                                  
REMARK 620 N                    1     2     3                                   
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                           1  ZN A   2  ZN                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 CYS A 220   SG                                                     
REMARK 620 2 CYS A 223   SG  107.1                                              
REMARK 620 3 CYS A 240   SG  107.1 109.9                                        
REMARK 620 4 CYS A 243   SG  111.6 114.3 106.6                                  
REMARK 620 N                    1     2     3                                   
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                           1  ZN A   3  ZN                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 CYS A 232   SG                                                     
REMARK 620 2 CYS A 235   SG  112.2                                              
REMARK 620 3 CYS A 265   SG  107.8 104.5                                        
REMARK 620 4 CYS A 268   SG  110.2 105.3 116.8                                  
REMARK 620 N                    1     2     3                                   
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1                    
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2                    
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC3                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 3                    
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 15001   RELATED DB: BMRB                                 
REMARK 900 CHEMICAL SHIFT ASSIGNMENTS                                           
DBREF  2JM1 A  156   296  UNP    P46100   ATRX_HUMAN     159    296             
SEQADV 2JM1 GLY A  156  UNP  P46100              CLONING ARTIFACT               
SEQADV 2JM1 ALA A  157  UNP  P46100              CLONING ARTIFACT               
SEQADV 2JM1 MET A  158  UNP  P46100              CLONING ARTIFACT               
SEQRES   1 A  141  GLY ALA MET LYS ARG GLY GLU ASP GLY LEU HIS GLY ILE          
SEQRES   2 A  141  VAL SER CYS THR ALA CYS GLY GLN GLN VAL ASN HIS PHE          
SEQRES   3 A  141  GLN LYS ASP SER ILE TYR ARG HIS PRO SER LEU GLN VAL          
SEQRES   4 A  141  LEU ILE CYS LYS ASN CYS PHE LYS TYR TYR MET SER ASP          
SEQRES   5 A  141  ASP ILE SER ARG ASP SER ASP GLY MET ASP GLU GLN CYS          
SEQRES   6 A  141  ARG TRP CYS ALA GLU GLY GLY ASN LEU ILE CYS CYS ASP          
SEQRES   7 A  141  PHE CYS HIS ASN ALA PHE CYS LYS LYS CYS ILE LEU ARG          
SEQRES   8 A  141  ASN LEU GLY ARG LYS GLU LEU SER THR ILE MET ASP GLU          
SEQRES   9 A  141  ASN ASN GLN TRP TYR CYS TYR ILE CYS HIS PRO GLU PRO          
SEQRES  10 A  141  LEU LEU ASP LEU VAL THR ALA CYS ASN SER VAL PHE GLU          
SEQRES  11 A  141  ASN LEU GLU GLN LEU LEU GLN GLN ASN LYS LYS                  
HET     ZN  A   1       1                                                       
HET     ZN  A   2       1                                                       
HET     ZN  A   3       1                                                       
HETNAM      ZN ZINC ION                                                         
FORMUL   2   ZN    3(ZN 2+)                                                     
HELIX    1   1 CYS A  197  ASP A  207  1                                  11    
HELIX    2   2 LYS A  241  GLY A  249  1                                   9    
HELIX    3   3 ARG A  250  MET A  257  1                                   8    
HELIX    4   4 LEU A  273  GLN A  292  1                                  20    
SHEET    1   A 2 TYR A 187  ARG A 188  0                                        
SHEET    2   A 2 LEU A 195  ILE A 196 -1  O  ILE A 196   N  TYR A 187           
SHEET    1   B 2 LEU A 229  CYS A 231  0                                        
SHEET    2   B 2 ALA A 238  CYS A 240 -1  O  PHE A 239   N  ILE A 230           
LINK        ZN    ZN A   1                 SG  CYS A 171     1555   1555  2.31  
LINK        ZN    ZN A   1                 SG  CYS A 174     1555   1555  2.31  
LINK        ZN    ZN A   1                 SG  CYS A 197     1555   1555  2.31  
LINK        ZN    ZN A   1                 SG  CYS A 200     1555   1555  2.30  
LINK        ZN    ZN A   2                 SG  CYS A 220     1555   1555  2.29  
LINK        ZN    ZN A   2                 SG  CYS A 223     1555   1555  2.31  
LINK        ZN    ZN A   2                 SG  CYS A 240     1555   1555  2.30  
LINK        ZN    ZN A   2                 SG  CYS A 243     1555   1555  2.31  
LINK        ZN    ZN A   3                 SG  CYS A 232     1555   1555  2.30  
LINK        ZN    ZN A   3                 SG  CYS A 235     1555   1555  2.30  
LINK        ZN    ZN A   3                 SG  CYS A 265     1555   1555  2.30  
LINK        ZN    ZN A   3                 SG  CYS A 268     1555   1555  2.31  
SITE     1 AC1  4 CYS A 171  CYS A 174  CYS A 197  CYS A 200                    
SITE     1 AC2  4 CYS A 220  CYS A 223  CYS A 240  CYS A 243                    
SITE     1 AC3  4 CYS A 232  CYS A 235  CYS A 265  CYS A 268                    
CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1          
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      1.000000  0.000000  0.000000        0.00000                         
SCALE2      0.000000  1.000000  0.000000        0.00000                         
SCALE3      0.000000  0.000000  1.000000        0.00000