PDB Short entry for 2LD1
HEADER    METAL BINDING PROTEIN                   13-MAY-11   2LD1              
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: 3.6.4.12;                                                        
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: PET30A                                     
KEYWDS    HYDROLASE, METAL BINDING PROTEIN                                      
EXPDTA    SOLUTION NMR                                                          
NUMMDL    34                                                                    
AUTHOR    D.NEUHAUS,J.YANG                                                      
REVDAT   1   08-JUN-11 2LD1    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     : BRUNGER                                              
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 2LD1 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAY-11.                  
REMARK 100 THE RCSB ID CODE IS RCSB102247.                                      
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                : 0.6-0.8 MM [U-15N] ADD_DOMAIN_     
REMARK 210                                   163-296, 20 MM [U-2H] TRIS, 1 MM   
REMARK 210                                   [U-2H] DTT, 100 UM ZINC CHLORIDE,  
REMARK 210                                   0.5 M SODIUM CHLORIDE, 95% H2O/5%  
REMARK 210                                   D2O; 0.3-0.4 MM [U-13C; U-15N]     
REMARK 210                                   ADD_DOMAIN_163-296, 20 MM [U-2H]   
REMARK 210                                   TRIS, 1 MM [U-2H] DTT, 100 UM      
REMARK 210                                   ZINC CHLORIDE, 0.5 M SODIUM        
REMARK 210                                   CHLORIDE, 95% H2O/5% D2O           
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 2D 1H-15N HSQC; 2D 1H-1H NOESY;    
REMARK 210                                   3D 1H-15N NOESY; 3D HNHB; 2D 1H-   
REMARK 210                                   13C HSQC; 3D HNCACB; 3D HN(CO)     
REMARK 210                                   CACB; 3D HNHAHB; 3D HN(CO)HAHB;    
REMARK 210                                   3D HCCH-TOCSY; 3D HCCH-COSY; 3D    
REMARK 210                                   1H-13C 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    : 34                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : STRUCTURES WITH THE 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 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 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 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 LEU A 165       84.78     52.96                                   
REMARK 500  1 ASN A 179       93.63    -52.23                                   
REMARK 500  1 HIS A 180     -174.84     50.70                                   
REMARK 500  1 SER A 185      -69.20    -94.86                                   
REMARK 500  1 ILE A 186      159.19    -49.64                                   
REMARK 500  1 SER A 210      129.15   -173.04                                   
REMARK 500  1 SER A 213      -73.45     61.27                                   
REMARK 500  1 GLU A 218       56.62   -151.37                                   
REMARK 500  1 TRP A 222      -59.73   -151.65                                   
REMARK 500  1 ASN A 228       86.50     52.23                                   
REMARK 500  1 PHE A 234      -60.67   -149.66                                   
REMARK 500  1 LEU A 248       25.18   -146.31                                   
REMARK 500  1 ASP A 258       62.16   -168.37                                   
REMARK 500  1 GLU A 259      -66.73   -129.37                                   
REMARK 500  1 ASN A 260       36.51   -152.16                                   
REMARK 500  1 CYS A 265     -148.64   -126.48                                   
REMARK 500  1 PRO A 270       73.21    -68.97                                   
REMARK 500  1 LEU A 273       35.20   -155.86                                   
REMARK 500  1 GLN A 293       60.48   -106.68                                   
REMARK 500  2 ARG A 161      -64.12   -137.85                                   
REMARK 500  2 ASN A 179       92.57    -53.41                                   
REMARK 500  2 HIS A 180     -175.46     50.70                                   
REMARK 500  2 ARG A 211       89.84     51.82                                   
REMARK 500  2 ASP A 214       37.99   -150.52                                   
REMARK 500  2 MET A 216       35.43   -143.74                                   
REMARK 500  2 ASP A 217      103.47     55.17                                   
REMARK 500  2 TRP A 222      -59.75   -150.99                                   
REMARK 500  2 ASN A 228       84.93     52.06                                   
REMARK 500  2 ASP A 233       40.77   -106.77                                   
REMARK 500  2 PHE A 234      -57.78   -152.05                                   
REMARK 500  2 LEU A 248       24.91   -146.08                                   
REMARK 500  2 ASP A 258       64.53   -169.24                                   
REMARK 500  2 GLU A 259      -67.43   -129.68                                   
REMARK 500  2 ASN A 260       37.03   -152.60                                   
REMARK 500  2 CYS A 265     -148.56   -123.96                                   
REMARK 500  2 PRO A 270       73.82    -68.72                                   
REMARK 500  2 LEU A 273       35.79   -156.38                                   
REMARK 500  2 GLN A 293       60.84   -103.15                                   
REMARK 500  3 ARG A 161      -65.01   -136.52                                   
REMARK 500  3 ASP A 163       40.56   -142.50                                   
REMARK 500  3 LEU A 165      -59.83   -143.65                                   
REMARK 500  3 ASN A 179       93.26    -53.57                                   
REMARK 500  3 HIS A 180     -175.39     50.92                                   
REMARK 500  3 SER A 185      -69.48    -91.61                                   
REMARK 500  3 SER A 210      124.22   -171.03                                   
REMARK 500  3 ARG A 211       74.37     52.17                                   
REMARK 500  3 SER A 213      -70.53     64.82                                   
REMARK 500  3 GLU A 218       50.45   -141.37                                   
REMARK 500  3 TRP A 222      -59.71   -150.39                                   
REMARK 500  3 ASN A 228       93.36     52.41                                   
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS     636 RAMACHANDRAN OUTLIERS.                        
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   2  ZN                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 CYS A 220   SG                                                     
REMARK 620 2 CYS A 240   SG  107.5                                              
REMARK 620 3 CYS A 243   SG  112.0 106.3                                        
REMARK 620 4 CYS A 223   SG  107.1 109.9 113.9                                  
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 265   SG  106.7                                              
REMARK 620 3 CYS A 235   SG  112.6 104.4                                        
REMARK 620 4 CYS A 268   SG  109.2 117.6 106.4                                  
REMARK 620 N                    1     2     3                                   
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 200   SG                                                     
REMARK 620 2 CYS A 174   SG  103.1                                              
REMARK 620 3 CYS A 171   SG  109.6 112.6                                        
REMARK 620 4 CYS A 197   SG  109.6 110.1 111.5                                  
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 NMR CHEMICAL SHIFT ASSIGNMENTS FOR ATRX ADD DOMAIN                   
DBREF  2LD1 A  160   296  UNP    P46100   ATRX_HUMAN     159    296             
SEQADV 2LD1 GLY A  155  UNP  P46100              EXPRESSION TAG                 
SEQADV 2LD1 ALA A  156  UNP  P46100              EXPRESSION TAG                 
SEQADV 2LD1 MET A  157  UNP  P46100              EXPRESSION TAG                 
SEQADV 2LD1 ALA A  158  UNP  P46100              EXPRESSION TAG                 
SEQADV 2LD1 ASP A  159  UNP  P46100              EXPRESSION TAG                 
SEQADV 2LD1     A       UNP  P46100    GLU   162 DELETION                       
SEQRES   1 A  142  GLY ALA MET ALA ASP LYS ARG GLY ASP GLY LEU HIS GLY          
SEQRES   2 A  142  ILE VAL SER CYS THR ALA CYS GLY GLN GLN VAL ASN HIS          
SEQRES   3 A  142  PHE GLN LYS ASP SER ILE TYR ARG HIS PRO SER LEU GLN          
SEQRES   4 A  142  VAL LEU ILE CYS LYS ASN CYS PHE LYS TYR TYR MET SER          
SEQRES   5 A  142  ASP ASP ILE SER ARG ASP SER ASP GLY MET ASP GLU GLN          
SEQRES   6 A  142  CYS ARG TRP CYS ALA GLU GLY GLY ASN LEU ILE CYS CYS          
SEQRES   7 A  142  ASP PHE CYS HIS ASN ALA PHE CYS LYS LYS CYS ILE LEU          
SEQRES   8 A  142  ARG ASN LEU GLY ARG LYS GLU LEU SER THR ILE MET ASP          
SEQRES   9 A  142  GLU ASN ASN GLN TRP TYR CYS TYR ILE CYS HIS PRO GLU          
SEQRES  10 A  142  PRO LEU LEU ASP LEU VAL THR ALA CYS ASN SER VAL PHE          
SEQRES  11 A  142  GLU 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  293  1                                  21    
SHEET    1   A 2 SER A 170  CYS A 171  0                                        
SHEET    2   A 2 GLN A 176  GLN A 177 -1  O  GLN A 176   N  CYS A 171           
SHEET    1   B 2 TYR A 187  ARG A 188  0                                        
SHEET    2   B 2 LEU A 195  ILE A 196 -1  O  ILE A 196   N  TYR A 187           
SHEET    1   C 2 LEU A 229  CYS A 231  0                                        
SHEET    2   C 2 ALA A 238  CYS A 240 -1  O  PHE A 239   N  ILE A 230           
LINK         SG  CYS A 220                ZN    ZN A   2     1555   1555  2.29  
LINK         SG  CYS A 232                ZN    ZN A   3     1555   1555  2.30  
LINK         SG  CYS A 265                ZN    ZN A   3     1555   1555  2.30  
LINK         SG  CYS A 240                ZN    ZN A   2     1555   1555  2.30  
LINK         SG  CYS A 200                ZN    ZN A   1     1555   1555  2.30  
LINK         SG  CYS A 235                ZN    ZN A   3     1555   1555  2.30  
LINK         SG  CYS A 174                ZN    ZN A   1     1555   1555  2.30  
LINK         SG  CYS A 171                ZN    ZN A   1     1555   1555  2.31  
LINK         SG  CYS A 268                ZN    ZN A   3     1555   1555  2.31  
LINK         SG  CYS A 197                ZN    ZN A   1     1555   1555  2.31  
LINK         SG  CYS A 243                ZN    ZN A   2     1555   1555  2.31  
LINK         SG  CYS A 223                ZN    ZN A   2     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