PDB Short entry for 5C11 HEADER HYDROLASE 12-JUN-15 5C11 TITLE CRYSTAL STRUCTURE OF JARID1A PHD FINGER BOUND TO HISTONE H3C4ME3 TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 5A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PHD FINGER DOMAIN, UNP RESIDUES 1609-1659; COMPND 5 SYNONYM: HISTONE DEMETHYLASE JARID1A,JUMONJI/ARID DOMAIN-CONTAINING COMPND 6 PROTEIN 1A,RETINOBLASTOMA-BINDING PROTEIN 2,RBBP-2; COMPND 7 EC: 1.14.11.-; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: H3 PEPTIDE; COMPND 11 CHAIN: B; COMPND 12 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: KDM5A, JARID1A, RBBP2, RBP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); 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: PET28B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 OTHER_DETAILS: CHEMICALLY SYNTHESIZED H3 PEPTIDE 1-10 WITH K4CME3 SOURCE 16 MODIFICATION KEYWDS ZINC FINGER PROTEIN, DEMETHYLASE, READER MODULE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.HUANG,H.LI REVDAT 4 15-NOV-23 5C11 1 REMARK REVDAT 3 08-NOV-23 5C11 1 REMARK REVDAT 2 27-SEP-17 5C11 1 REMARK REVDAT 1 25-NOV-15 5C11 0 JRNL AUTH J.HUANG,H.LI JRNL TITL CRYSTAL STRUCTURE OF JARID1A PHD FINGER BOUND TO HISTONE JRNL TITL 2 H3C4ME3 PEPTIDE JRNL REF NAT COMMUN 2015 JRNL REFN ESSN 2041-1723 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.470 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 2920 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.248 REMARK 3 R VALUE (WORKING SET) : 0.246 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.520 REMARK 3 FREE R VALUE TEST SET COUNT : 278 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 44.4679 - 3.5309 0.99 1368 136 0.2392 0.2656 REMARK 3 2 3.5309 - 2.8027 1.00 1274 142 0.2746 0.3317 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 96.56 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 95.21 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 : 0.003 463 REMARK 3 ANGLE : 0.698 627 REMARK 3 CHIRALITY : 0.030 65 REMARK 3 PLANARITY : 0.002 84 REMARK 3 DIHEDRAL : 15.304 171 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 5C11 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000210852. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-SEP-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL, SI(111) REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2920 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 17.10 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.40 REMARK 200 R MERGE FOR SHELL (I) : 0.79800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 11.2.05 REMARK 200 STARTING MODEL: 3GL6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.02 M SODIUM L-GLUTAMATE, 0.02 M DL REMARK 280 -ALANINE, 0.02 M GLYCINE, 0.02 M DL-LYSINE HCL, 0.02 M DL-SERINE, REMARK 280 0.1 M TRIS, 0.1 M BICINE, PH8.5, 12.5% MPD, 12.5% PEG 1K, 12.5% REMARK 280 PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X REMARK 290 13555 Y,X,-Z REMARK 290 14555 -Y,-X,-Z REMARK 290 15555 Y,-X,Z REMARK 290 16555 -Y,X,Z REMARK 290 17555 X,Z,-Y REMARK 290 18555 -X,Z,Y REMARK 290 19555 -X,-Z,-Y REMARK 290 20555 X,-Z,Y REMARK 290 21555 Z,Y,-X REMARK 290 22555 Z,-Y,X REMARK 290 23555 -Z,Y,X REMARK 290 24555 -Z,-Y,-X REMARK 290 25555 X+1/2,Y+1/2,Z+1/2 REMARK 290 26555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 27555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 28555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 29555 Z+1/2,X+1/2,Y+1/2 REMARK 290 30555 Z+1/2,-X+1/2,-Y+1/2 REMARK 290 31555 -Z+1/2,-X+1/2,Y+1/2 REMARK 290 32555 -Z+1/2,X+1/2,-Y+1/2 REMARK 290 33555 Y+1/2,Z+1/2,X+1/2 REMARK 290 34555 -Y+1/2,Z+1/2,-X+1/2 REMARK 290 35555 Y+1/2,-Z+1/2,-X+1/2 REMARK 290 36555 -Y+1/2,-Z+1/2,X+1/2 REMARK 290 37555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 38555 -Y+1/2,-X+1/2,-Z+1/2 REMARK 290 39555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 40555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 41555 X+1/2,Z+1/2,-Y+1/2 REMARK 290 42555 -X+1/2,Z+1/2,Y+1/2 REMARK 290 43555 -X+1/2,-Z+1/2,-Y+1/2 REMARK 290 44555 X+1/2,-Z+1/2,Y+1/2 REMARK 290 45555 Z+1/2,Y+1/2,-X+1/2 REMARK 290 46555 Z+1/2,-Y+1/2,X+1/2 REMARK 290 47555 -Z+1/2,Y+1/2,X+1/2 REMARK 290 48555 -Z+1/2,-Y+1/2,-X+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 13 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 14 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 16 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 16 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 17 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 18 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 18 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 18 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 19 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 19 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 19 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 20 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 20 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 20 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 21 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 21 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 21 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 22 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 22 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 22 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 23 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 23 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 23 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 24 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 24 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 24 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 25 1.000000 0.000000 0.000000 54.45500 REMARK 290 SMTRY2 25 0.000000 1.000000 0.000000 54.45500 REMARK 290 SMTRY3 25 0.000000 0.000000 1.000000 54.45500 REMARK 290 SMTRY1 26 -1.000000 0.000000 0.000000 54.45500 REMARK 290 SMTRY2 26 0.000000 -1.000000 0.000000 54.45500 REMARK 290 SMTRY3 26 0.000000 0.000000 1.000000 54.45500 REMARK 290 SMTRY1 27 -1.000000 0.000000 0.000000 54.45500 REMARK 290 SMTRY2 27 0.000000 1.000000 0.000000 54.45500 REMARK 290 SMTRY3 27 0.000000 0.000000 -1.000000 54.45500 REMARK 290 SMTRY1 28 1.000000 0.000000 0.000000 54.45500 REMARK 290 SMTRY2 28 0.000000 -1.000000 0.000000 54.45500 REMARK 290 SMTRY3 28 0.000000 0.000000 -1.000000 54.45500 REMARK 290 SMTRY1 29 0.000000 0.000000 1.000000 54.45500 REMARK 290 SMTRY2 29 1.000000 0.000000 0.000000 54.45500 REMARK 290 SMTRY3 29 0.000000 1.000000 0.000000 54.45500 REMARK 290 SMTRY1 30 0.000000 0.000000 1.000000 54.45500 REMARK 290 SMTRY2 30 -1.000000 0.000000 0.000000 54.45500 REMARK 290 SMTRY3 30 0.000000 -1.000000 0.000000 54.45500 REMARK 290 SMTRY1 31 0.000000 0.000000 -1.000000 54.45500 REMARK 290 SMTRY2 31 -1.000000 0.000000 0.000000 54.45500 REMARK 290 SMTRY3 31 0.000000 1.000000 0.000000 54.45500 REMARK 290 SMTRY1 32 0.000000 0.000000 -1.000000 54.45500 REMARK 290 SMTRY2 32 1.000000 0.000000 0.000000 54.45500 REMARK 290 SMTRY3 32 0.000000 -1.000000 0.000000 54.45500 REMARK 290 SMTRY1 33 0.000000 1.000000 0.000000 54.45500 REMARK 290 SMTRY2 33 0.000000 0.000000 1.000000 54.45500 REMARK 290 SMTRY3 33 1.000000 0.000000 0.000000 54.45500 REMARK 290 SMTRY1 34 0.000000 -1.000000 0.000000 54.45500 REMARK 290 SMTRY2 34 0.000000 0.000000 1.000000 54.45500 REMARK 290 SMTRY3 34 -1.000000 0.000000 0.000000 54.45500 REMARK 290 SMTRY1 35 0.000000 1.000000 0.000000 54.45500 REMARK 290 SMTRY2 35 0.000000 0.000000 -1.000000 54.45500 REMARK 290 SMTRY3 35 -1.000000 0.000000 0.000000 54.45500 REMARK 290 SMTRY1 36 0.000000 -1.000000 0.000000 54.45500 REMARK 290 SMTRY2 36 0.000000 0.000000 -1.000000 54.45500 REMARK 290 SMTRY3 36 1.000000 0.000000 0.000000 54.45500 REMARK 290 SMTRY1 37 0.000000 1.000000 0.000000 54.45500 REMARK 290 SMTRY2 37 1.000000 0.000000 0.000000 54.45500 REMARK 290 SMTRY3 37 0.000000 0.000000 -1.000000 54.45500 REMARK 290 SMTRY1 38 0.000000 -1.000000 0.000000 54.45500 REMARK 290 SMTRY2 38 -1.000000 0.000000 0.000000 54.45500 REMARK 290 SMTRY3 38 0.000000 0.000000 -1.000000 54.45500 REMARK 290 SMTRY1 39 0.000000 1.000000 0.000000 54.45500 REMARK 290 SMTRY2 39 -1.000000 0.000000 0.000000 54.45500 REMARK 290 SMTRY3 39 0.000000 0.000000 1.000000 54.45500 REMARK 290 SMTRY1 40 0.000000 -1.000000 0.000000 54.45500 REMARK 290 SMTRY2 40 1.000000 0.000000 0.000000 54.45500 REMARK 290 SMTRY3 40 0.000000 0.000000 1.000000 54.45500 REMARK 290 SMTRY1 41 1.000000 0.000000 0.000000 54.45500 REMARK 290 SMTRY2 41 0.000000 0.000000 1.000000 54.45500 REMARK 290 SMTRY3 41 0.000000 -1.000000 0.000000 54.45500 REMARK 290 SMTRY1 42 -1.000000 0.000000 0.000000 54.45500 REMARK 290 SMTRY2 42 0.000000 0.000000 1.000000 54.45500 REMARK 290 SMTRY3 42 0.000000 1.000000 0.000000 54.45500 REMARK 290 SMTRY1 43 -1.000000 0.000000 0.000000 54.45500 REMARK 290 SMTRY2 43 0.000000 0.000000 -1.000000 54.45500 REMARK 290 SMTRY3 43 0.000000 -1.000000 0.000000 54.45500 REMARK 290 SMTRY1 44 1.000000 0.000000 0.000000 54.45500 REMARK 290 SMTRY2 44 0.000000 0.000000 -1.000000 54.45500 REMARK 290 SMTRY3 44 0.000000 1.000000 0.000000 54.45500 REMARK 290 SMTRY1 45 0.000000 0.000000 1.000000 54.45500 REMARK 290 SMTRY2 45 0.000000 1.000000 0.000000 54.45500 REMARK 290 SMTRY3 45 -1.000000 0.000000 0.000000 54.45500 REMARK 290 SMTRY1 46 0.000000 0.000000 1.000000 54.45500 REMARK 290 SMTRY2 46 0.000000 -1.000000 0.000000 54.45500 REMARK 290 SMTRY3 46 1.000000 0.000000 0.000000 54.45500 REMARK 290 SMTRY1 47 0.000000 0.000000 -1.000000 54.45500 REMARK 290 SMTRY2 47 0.000000 1.000000 0.000000 54.45500 REMARK 290 SMTRY3 47 1.000000 0.000000 0.000000 54.45500 REMARK 290 SMTRY1 48 0.000000 0.000000 -1.000000 54.45500 REMARK 290 SMTRY2 48 0.000000 -1.000000 0.000000 54.45500 REMARK 290 SMTRY3 48 -1.000000 0.000000 0.000000 54.45500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 ARG B 8 REMARK 465 LYS B 9 REMARK 465 SER B 10 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 ASN A 7 70.91 -108.08 REMARK 500 ARG A 10 68.04 32.32 REMARK 500 LYS A 15 106.76 70.85 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 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 3 SG REMARK 620 2 CYS A 8 SG 109.2 REMARK 620 3 HIS A 30 ND1 106.2 102.7 REMARK 620 4 CYS A 33 SG 111.3 119.5 106.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 21 SG REMARK 620 2 CYS A 25 SG 124.0 REMARK 620 3 CYS A 48 SG 101.6 121.0 REMARK 620 4 CYS A 51 SG 97.6 109.6 97.7 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 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Ligand residues 4WQ B 4 through REMARK 800 GLN B 5 bound to THR B 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5C13 RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE OF THE ENTITY2 OF THIS PROTEIN WAS NOT AVAILABLE AT REMARK 999 THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF REMARK 999 DEPOSITION. DBREF 5C11 A 2 52 UNP P29375 KDM5A_HUMAN 1609 1659 DBREF 5C11 B 1 10 PDB 5C11 5C11 1 10 SEQADV 5C11 SER A 1 UNP P29375 EXPRESSION TAG SEQRES 1 A 52 SER VAL CYS ALA ALA GLN ASN CYS GLN ARG PRO CYS LYS SEQRES 2 A 52 ASP LYS VAL ASP TRP VAL GLN CYS ASP GLY GLY CYS ASP SEQRES 3 A 52 GLU TRP PHE HIS GLN VAL CYS VAL GLY VAL SER PRO GLU SEQRES 4 A 52 MET ALA GLU ASN GLU ASP TYR ILE CYS ILE ASN CYS ALA SEQRES 1 B 10 ALA ARG THR 4WQ GLN THR ALA ARG LYS SER HET 4WQ B 4 12 HET ZN A 101 1 HET ZN A 102 1 HETNAM 4WQ (2S)-2-AMINO-7,7-DIMETHYLOCTANOIC ACID HETNAM ZN ZINC ION FORMUL 2 4WQ C10 H21 N O2 FORMUL 3 ZN 2(ZN 2+) HELIX 1 AA1 VAL A 32 GLY A 35 5 4 HELIX 2 AA2 SER A 37 GLU A 44 1 8 SHEET 1 AA1 3 TRP A 28 HIS A 30 0 SHEET 2 AA1 3 VAL A 16 GLN A 20 -1 N VAL A 19 O PHE A 29 SHEET 3 AA1 3 THR B 3 THR B 6 -1 O 4WQ B 4 N TRP A 18 SSBOND 1 CYS A 12 CYS A 12 1555 18455 2.03 LINK C THR B 3 N 4WQ B 4 1555 1555 1.33 LINK C 4WQ B 4 N GLN B 5 1555 1555 1.33 LINK SG CYS A 3 ZN ZN A 101 1555 1555 2.35 LINK SG CYS A 8 ZN ZN A 101 1555 1555 2.40 LINK SG CYS A 21 ZN ZN A 102 1555 1555 2.41 LINK SG CYS A 25 ZN ZN A 102 1555 1555 2.35 LINK ND1 HIS A 30 ZN ZN A 101 1555 1555 2.06 LINK SG CYS A 33 ZN ZN A 101 1555 1555 2.36 LINK SG CYS A 48 ZN ZN A 102 1555 1555 2.39 LINK SG CYS A 51 ZN ZN A 102 1555 1555 2.39 SITE 1 AC1 4 CYS A 3 CYS A 8 HIS A 30 CYS A 33 SITE 1 AC2 4 CYS A 21 CYS A 25 CYS A 48 CYS A 51 SITE 1 AC3 6 VAL A 16 ASP A 17 TRP A 18 TRP A 28 SITE 2 AC3 6 THR B 3 THR B 6 CRYST1 108.910 108.910 108.910 90.00 90.00 90.00 I 4 3 2 48 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 0.009182 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009182 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009182 0.00000