HEADER    OXIDOREDUCTASE                          16-APR-14   2MNY              
TITLE     NMR STRUCTURE OF KDM5B PHD1 FINGER                                    
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 5B;                            
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: ZINC FINGER DOMAIN PHD1, RESIDUES 306-360;                 
COMPND   5 SYNONYM: CANCER/TESTIS ANTIGEN 31, CT31, HISTONE DEMETHYLASE JARID1B,
COMPND   6 JUMONJI/ARID DOMAIN-CONTAINING PROTEIN 1B, PLU-1, RETINOBLASTOMA-    
COMPND   7 BINDING PROTEIN 2 HOMOLOG 1, RBP2-H1;                                
COMPND   8 EC: 1.14.11.-;                                                       
COMPND   9 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: KDM5B;                                                         
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);                                 
SOURCE   9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR;                               
SOURCE  10 EXPRESSION_SYSTEM_VECTOR: PGEX-6P-1                                  
KEYWDS    PHD1, KDM5B, H3K4, DEMETHYLATION, OXIDOREDUCTASE                      
EXPDTA    SOLUTION NMR                                                          
NUMMDL    20                                                                    
AUTHOR    Y.ZHANG,H.R.YANG,X.GUO,N.Y.RONG,Y.J.SONG,Y.W.XU,W.X.LAN,Y.H.XU,C.CAO  
REVDAT   4   15-MAY-24 2MNY    1       REMARK                                   
REVDAT   3   14-JUN-23 2MNY    1       REMARK                                   
REVDAT   2   24-AUG-22 2MNY    1       JRNL   REMARK LINK                       
REVDAT   1   06-AUG-14 2MNY    0                                                
JRNL        AUTH   Y.ZHANG,H.YANG,X.GUO,N.RONG,Y.SONG,Y.XU,W.LAN,X.ZHANG,M.LIU, 
JRNL        AUTH 2 Y.XU,C.CAO                                                   
JRNL        TITL   THE PHD1 FINGER OF KDM5B RECOGNIZES UNMODIFIED H3K4 DURING   
JRNL        TITL 2 THE DEMETHYLATION OF HISTONE H3K4ME2/3 BY KDM5B.             
JRNL        REF    PROTEIN CELL                  V.   5   837 2014              
JRNL        REFN                   ESSN 1674-8018                               
JRNL        PMID   24952722                                                     
JRNL        DOI    10.1007/S13238-014-0078-4                                    
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : CNS                                                  
REMARK   3   AUTHORS     : BRUNGER A. T. ET.AL.                                 
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 2MNY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-APR-14.                  
REMARK 100 THE DEPOSITION ID IS D_1000103842.                                   
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 293                                
REMARK 210  PH                             : 7.2                                
REMARK 210  IONIC STRENGTH                 : 100                                
REMARK 210  PRESSURE                       : 1 ATM                              
REMARK 210  SAMPLE CONTENTS                : 0.8 MM [U-13C; U-15N] PHD1         
REMARK 210                                   FINGER OF KDM5B-1, 90% H2O, 10%    
REMARK 210                                   D2O; 0.8 MM [U-13C; U-15N] PHD1    
REMARK 210                                   FINGER OF KDM5B-2, 100% D2O        
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 3D_15N-SEPARATED_NOESY; 3D         
REMARK 210                                   CBCA(CO)NH; 2D 1H-15N HSQC; 3D     
REMARK 210                                   HNCO; 3D 1H-15N TOCSY; 3D HNCA;    
REMARK 210                                   3D HNCACB; 3D 1H-13C NOESY         
REMARK 210                                   ALIPHATIC; 3D 1H-13C NOESY         
REMARK 210                                   AROMATIC; 3D HCCH-TOCSY; 2D 1H-    
REMARK 210                                   13C HSQC AROMATIC; 2D 1H-13C       
REMARK 210                                   HSQC ALIPHATIC                     
REMARK 210  SPECTROMETER FIELD STRENGTH    : 600 MHZ                            
REMARK 210  SPECTROMETER MODEL             : DD2                                
REMARK 210  SPECTROMETER MANUFACTURER      : AGILENT                            
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : NULL                               
REMARK 210   METHOD USED                   : SIMULATED ANNEALING                
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 100                                
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 20                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : STRUCTURES WITH THE LOWEST         
REMARK 210                                   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: CLOSE CONTACTS                                             
REMARK 500                                                                      
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.                            
REMARK 500                                                                      
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE          
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
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 CYS A 315      -59.68   -128.51                                   
REMARK 500  1 LEU A 339      -45.26   -174.34                                   
REMARK 500  1 PRO A 342      162.87    -34.70                                   
REMARK 500  1 LEU A 343     -129.49   -137.02                                   
REMARK 500  2 CYS A 315      -66.02   -128.01                                   
REMARK 500  2 ASP A 331       89.20    -68.16                                   
REMARK 500  2 LEU A 339      -43.40   -175.05                                   
REMARK 500  2 PRO A 342      164.03    -36.51                                   
REMARK 500  2 LEU A 343      -95.83   -123.14                                   
REMARK 500  3 ASP A 331       12.84    -60.41                                   
REMARK 500  3 LEU A 339      -39.46   -175.34                                   
REMARK 500  3 PRO A 342      162.29    -34.75                                   
REMARK 500  3 LEU A 343     -138.56   -123.51                                   
REMARK 500  4 CYS A 330     -145.41   -152.63                                   
REMARK 500  4 LEU A 339      -36.75   -151.51                                   
REMARK 500  4 PRO A 342      159.86    -34.67                                   
REMARK 500  4 LYS A 348      -56.85   -163.43                                   
REMARK 500  5 TYR A 310      108.24     58.22                                   
REMARK 500  5 ASP A 331       14.03    -60.40                                   
REMARK 500  5 LEU A 339      -45.47   -173.92                                   
REMARK 500  5 PRO A 342      163.91    -36.29                                   
REMARK 500  5 LEU A 343      -42.81   -172.07                                   
REMARK 500  6 CYS A 315       28.95   -153.39                                   
REMARK 500  6 CYS A 330     -140.20   -142.46                                   
REMARK 500  6 LEU A 339      -31.42   -153.80                                   
REMARK 500  6 PRO A 342      162.69    -35.41                                   
REMARK 500  6 LEU A 343      -34.42   -131.58                                   
REMARK 500  7 ASP A 331       86.83    -68.73                                   
REMARK 500  7 LEU A 339      -46.25   -175.63                                   
REMARK 500  7 PRO A 342      163.63    -34.79                                   
REMARK 500  7 LYS A 348     -125.46   -173.24                                   
REMARK 500  8 CYS A 315      -46.98   -151.63                                   
REMARK 500  8 CYS A 330     -156.78   -142.55                                   
REMARK 500  8 LEU A 339      -34.35   -150.15                                   
REMARK 500  8 PRO A 342      163.72    -33.87                                   
REMARK 500  8 LEU A 343      -60.73    179.87                                   
REMARK 500  9 CYS A 315      -41.98   -147.45                                   
REMARK 500  9 LEU A 339      -31.68   -164.76                                   
REMARK 500  9 PRO A 342      161.32    -34.78                                   
REMARK 500  9 LEU A 343     -121.97   -138.11                                   
REMARK 500 10 CYS A 330     -153.60   -149.71                                   
REMARK 500 10 LEU A 339      -46.77   -174.72                                   
REMARK 500 10 PRO A 342      161.52    -33.93                                   
REMARK 500 11 CYS A 315      -53.23   -125.34                                   
REMARK 500 11 LEU A 339      -45.73   -175.00                                   
REMARK 500 11 PRO A 342      161.80    -33.54                                   
REMARK 500 11 LEU A 343     -129.08   -137.03                                   
REMARK 500 12 SER A 317      -84.74    -83.42                                   
REMARK 500 12 CYS A 330     -160.55   -127.78                                   
REMARK 500 12 PRO A 342      159.86    -28.34                                   
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS      88 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                              ZN A 401  ZN                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 CYS A 312   SG                                                     
REMARK 620 2 CYS A 315   SG  108.3                                              
REMARK 620 3 HIS A 335   ND1 108.5 112.8                                        
REMARK 620 4 CYS A 338   SG  108.8 108.5 109.8                                  
REMARK 620 N                    1     2     3                                   
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              ZN A 402  ZN                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 CYS A 327   SG                                                     
REMARK 620 2 CYS A 330   SG  108.2                                              
REMARK 620 3 CYS A 353   SG  109.3 111.6                                        
REMARK 620 4 CYS A 356   SG  112.6 112.3 102.7                                  
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 401                  
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 402                  
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 19913   RELATED DB: BMRB                                 
REMARK 900 RELATED ID: 2MNZ   RELATED DB: PDB                                   
DBREF  2MNY A  306   360  UNP    Q9UGL1   KDM5B_HUMAN    306    360             
SEQRES   1 A   55  ALA VAL ASP LEU TYR VAL CYS LEU LEU CYS GLY SER GLY          
SEQRES   2 A   55  ASN ASP GLU ASP ARG LEU LEU LEU CYS ASP GLY CYS ASP          
SEQRES   3 A   55  ASP SER TYR HIS THR PHE CYS LEU ILE PRO PRO LEU HIS          
SEQRES   4 A   55  ASP VAL PRO LYS GLY ASP TRP ARG CYS PRO LYS CYS LEU          
SEQRES   5 A   55  ALA GLN GLU                                                  
HET     ZN  A 401       1                                                       
HET     ZN  A 402       1                                                       
HETNAM      ZN ZINC ION                                                         
FORMUL   2   ZN    2(ZN 2+)                                                     
HELIX    1   1 GLY A  318  ASP A  322  5                                   5    
HELIX    2   2 CYS A  353  GLU A  360  1                                   8    
SHEET    1   A 2 LEU A 324  LEU A 326  0                                        
SHEET    2   A 2 SER A 333  HIS A 335 -1  O  TYR A 334   N  LEU A 325           
LINK         SG  CYS A 312                ZN    ZN A 401     1555   1555  2.30  
LINK         SG  CYS A 315                ZN    ZN A 401     1555   1555  2.31  
LINK         SG  CYS A 327                ZN    ZN A 402     1555   1555  2.29  
LINK         SG  CYS A 330                ZN    ZN A 402     1555   1555  2.30  
LINK         ND1 HIS A 335                ZN    ZN A 401     1555   1555  2.01  
LINK         SG  CYS A 338                ZN    ZN A 401     1555   1555  2.31  
LINK         SG  CYS A 353                ZN    ZN A 402     1555   1555  2.31  
LINK         SG  CYS A 356                ZN    ZN A 402     1555   1555  2.29  
SITE     1 AC1  4 CYS A 312  CYS A 315  HIS A 335  CYS A 338                    
SITE     1 AC2  4 CYS A 327  CYS A 330  CYS A 353  CYS A 356                    
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                         
MODEL        1