HEADER H3K4ME3 BINDING PROTEIN, TRANSFERASE 29-NOV-09 3KVB TITLE STRUCTURE OF KIAA1718 JUMONJI DOMAIN IN COMPLEX WITH N-OXALYLGLYCINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 1D; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 92-488; COMPND 5 EC: 2.-.-.-; COMPND 6 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: JHDM1D, KIAA1718; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)CODONPLUS KEYWDS JUMONJI DOMAIN LYSINE DEMETHYLASE, METAL-BINDING, IRON, NICKEL ION, KEYWDS 2 H3K4ME3 BINDING PROTEIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.R.HORTON,A.K.UPADHYAY,H.H.QI,X.ZHANG,Y.SHI,X.CHENG REVDAT 3 06-SEP-23 3KVB 1 REMARK LINK REVDAT 2 09-FEB-10 3KVB 1 JRNL REVDAT 1 22-DEC-09 3KVB 0 JRNL AUTH J.R.HORTON,A.K.UPADHYAY,H.H.QI,X.ZHANG,Y.SHI,X.CHENG JRNL TITL ENZYMATIC AND STRUCTURAL INSIGHTS FOR SUBSTRATE SPECIFICITY JRNL TITL 2 OF A FAMILY OF JUMONJI HISTONE LYSINE DEMETHYLASES. JRNL REF NAT.STRUCT.MOL.BIOL. V. 17 38 2010 JRNL REFN ISSN 1545-9993 JRNL PMID 20023638 JRNL DOI 10.1038/NSMB.1753 REMARK 2 REMARK 2 RESOLUTION. 2.69 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 358678.440 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 14477 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 711 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.69 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.79 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1079 REMARK 3 BIN R VALUE (WORKING SET) : 0.2870 REMARK 3 BIN FREE R VALUE : 0.2790 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 58 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.037 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2930 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 38 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 10.87000 REMARK 3 B22 (A**2) : 10.87000 REMARK 3 B33 (A**2) : -21.73000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM SIGMAA (A) : 0.29 REMARK 3 LOW RESOLUTION CUTOFF (A) : 35.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.49 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.40 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.780 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.300 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.220 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.980 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.070 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 41.11 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3KVB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000056492. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15320 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.690 REMARK 200 RESOLUTION RANGE LOW (A) : 33.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 14.40 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.3 REMARK 200 DATA REDUNDANCY IN SHELL : 8.00 REMARK 200 R MERGE FOR SHELL (I) : 0.39400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3KV6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 17-20% (V/V) POLYETHYLENE GLYCOL 5000 REMARK 280 MME, 0.2 M CACL2, AND 0.1 M BISTRIS PH 6.4, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 96.36667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 192.73333 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 144.55000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 240.91667 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 48.18333 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 96.36667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 192.73333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 240.91667 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 144.55000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 48.18333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 KCAL/MOL 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 350 BIOMT1 2 0.500000 0.866025 0.000000 -39.15000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 67.80979 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 48.18333 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 SER A 92 REMARK 465 LEU A 93 REMARK 465 MET A 94 REMARK 465 LYS A 95 REMARK 465 LYS A 96 REMARK 465 ARG A 97 REMARK 465 ARG A 98 REMARK 465 ASN A 99 REMARK 465 TRP A 100 REMARK 465 HIS A 101 REMARK 465 ARG A 102 REMARK 465 HIS A 103 REMARK 465 ASP A 104 REMARK 465 TYR A 105 REMARK 465 THR A 106 REMARK 465 GLU A 107 REMARK 465 ILE A 108 REMARK 465 ASP A 109 REMARK 465 ASP A 110 REMARK 465 GLY A 111 REMARK 465 SER A 112 REMARK 465 LYS A 113 REMARK 465 GLY A 480 REMARK 465 LYS A 481 REMARK 465 PRO A 482 REMARK 465 VAL A 483 REMARK 465 LYS A 484 REMARK 465 SER A 485 REMARK 465 GLN A 486 REMARK 465 GLY A 487 REMARK 465 ILE A 488 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 153 CG CD CE NZ REMARK 470 ARG A 184 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 218 CG OD1 ND2 REMARK 470 LYS A 234 CG CD CE NZ REMARK 470 GLU A 240 CG CD OE1 OE2 REMARK 470 ARG A 418 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 445 CG CD CE NZ REMARK 470 ASP A 457 CG OD1 OD2 REMARK 470 LYS A 466 CG CD CE NZ REMARK 470 SER A 469 OG REMARK 470 ARG A 473 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 476 CG CD OE1 OE2 REMARK 470 GLU A 477 CG CD OE1 OE2 REMARK 470 GLU A 478 CG CD OE1 OE2 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 PRO A 175 -1.93 -52.14 REMARK 500 ASP A 232 31.48 -94.77 REMARK 500 ASP A 276 1.01 86.59 REMARK 500 ASP A 361 121.55 -36.00 REMARK 500 LYS A 389 68.87 63.00 REMARK 500 LEU A 393 12.99 -69.18 REMARK 500 GLU A 478 34.13 -70.19 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 NI A 489 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 282 NE2 REMARK 620 2 ASP A 284 OD1 92.0 REMARK 620 3 HIS A 354 NE2 83.0 94.0 REMARK 620 4 OGA A5798 O2' 101.3 161.7 100.2 REMARK 620 5 OGA A5798 O2 74.5 80.7 156.5 90.6 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 489 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 490 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OXY A 491 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OGA A 5798 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KV9 RELATED DB: PDB REMARK 900 STRUCTURE OF KIAA1718 JUMONJI DOMAIN REMARK 900 RELATED ID: 3KVA RELATED DB: PDB REMARK 900 STRUCTURE OF KIAA1718 JUMONJI DOMAIN IN COMPLEX WITH ALPHA- REMARK 900 KETOGLUTARATE REMARK 900 RELATED ID: 3KV4 RELATED DB: PDB REMARK 900 RELATED ID: 3KV6 RELATED DB: PDB REMARK 900 RELATED ID: 3KV5 RELATED DB: PDB DBREF 3KVB A 92 488 UNP Q6ZMT4 JHD1D_HUMAN 92 488 SEQRES 1 A 397 SER LEU MET LYS LYS ARG ARG ASN TRP HIS ARG HIS ASP SEQRES 2 A 397 TYR THR GLU ILE ASP ASP GLY SER LYS PRO VAL GLN ALA SEQRES 3 A 397 GLY THR ARG THR PHE ILE LYS GLU LEU ARG SER ARG VAL SEQRES 4 A 397 PHE PRO SER ALA ASP GLU ILE ILE ILE LYS MET HIS GLY SEQRES 5 A 397 SER GLN LEU THR GLN ARG TYR LEU GLU LYS HIS GLY PHE SEQRES 6 A 397 ASP VAL PRO ILE MET VAL PRO LYS LEU ASP ASP LEU GLY SEQRES 7 A 397 LEU ARG LEU PRO SER PRO THR PHE SER VAL MET ASP VAL SEQRES 8 A 397 GLU ARG TYR VAL GLY GLY ASP LYS VAL ILE ASP VAL ILE SEQRES 9 A 397 ASP VAL ALA ARG GLN ALA ASP SER LYS MET THR LEU HIS SEQRES 10 A 397 ASN TYR VAL LYS TYR PHE MET ASN PRO ASN ARG PRO LYS SEQRES 11 A 397 VAL LEU ASN VAL ILE SER LEU GLU PHE SER ASP THR LYS SEQRES 12 A 397 MET SER GLU LEU VAL GLU VAL PRO ASP ILE ALA LYS LYS SEQRES 13 A 397 LEU SER TRP VAL GLU ASN TYR TRP PRO ASP ASP SER VAL SEQRES 14 A 397 PHE PRO LYS PRO PHE VAL GLN LYS TYR CYS LEU MET GLY SEQRES 15 A 397 VAL GLN ASP SER TYR THR ASP PHE HIS ILE ASP PHE GLY SEQRES 16 A 397 GLY THR SER VAL TRP TYR HIS VAL LEU TRP GLY GLU LYS SEQRES 17 A 397 ILE PHE TYR LEU ILE LYS PRO THR ASP GLU ASN LEU ALA SEQRES 18 A 397 ARG TYR GLU SER TRP SER SER SER VAL THR GLN SER GLU SEQRES 19 A 397 VAL PHE PHE GLY ASP LYS VAL ASP LYS CYS TYR LYS CYS SEQRES 20 A 397 VAL VAL LYS GLN GLY HIS THR LEU PHE VAL PRO THR GLY SEQRES 21 A 397 TRP ILE HIS ALA VAL LEU THR SER GLN ASP CYS MET ALA SEQRES 22 A 397 PHE GLY GLY ASN PHE LEU HIS ASN LEU ASN ILE GLY MET SEQRES 23 A 397 GLN LEU ARG CYS TYR GLU MET GLU LYS ARG LEU LYS THR SEQRES 24 A 397 PRO ASP LEU PHE LYS PHE PRO PHE PHE GLU ALA ILE CYS SEQRES 25 A 397 TRP PHE VAL ALA LYS ASN LEU LEU GLU THR LEU LYS GLU SEQRES 26 A 397 LEU ARG GLU ASP GLY PHE GLN PRO GLN THR TYR LEU VAL SEQRES 27 A 397 GLN GLY VAL LYS ALA LEU HIS THR ALA LEU LYS LEU TRP SEQRES 28 A 397 MET LYS LYS GLU LEU VAL SER GLU HIS ALA PHE GLU ILE SEQRES 29 A 397 PRO ASP ASN VAL ARG PRO GLY HIS LEU ILE LYS GLU LEU SEQRES 30 A 397 SER LYS VAL ILE ARG ALA ILE GLU GLU GLU ASN GLY LYS SEQRES 31 A 397 PRO VAL LYS SER GLN GLY ILE HET NI A 489 1 HET NI A 490 1 HET OXY A 491 2 HET OGA A5798 10 HETNAM NI NICKEL (II) ION HETNAM OXY OXYGEN MOLECULE HETNAM OGA N-OXALYLGLYCINE FORMUL 2 NI 2(NI 2+) FORMUL 4 OXY O2 FORMUL 5 OGA C4 H5 N O5 FORMUL 6 HOH *38(H2 O) HELIX 1 1 THR A 119 ARG A 129 1 11 HELIX 2 2 SER A 133 ILE A 137 5 5 HELIX 3 3 THR A 147 GLY A 155 1 9 HELIX 4 4 SER A 178 GLY A 187 1 10 HELIX 5 5 LEU A 207 MET A 215 1 9 HELIX 6 6 THR A 233 VAL A 239 5 7 HELIX 7 7 PRO A 242 SER A 249 1 8 HELIX 8 8 SER A 249 TRP A 255 1 7 HELIX 9 9 ASP A 284 THR A 288 5 5 HELIX 10 10 THR A 307 SER A 319 1 13 HELIX 11 11 SER A 320 VAL A 326 5 7 HELIX 12 12 PHE A 327 VAL A 332 5 6 HELIX 13 13 ASN A 374 LYS A 389 1 16 HELIX 14 14 THR A 390 LYS A 395 5 6 HELIX 15 15 PHE A 398 GLU A 419 1 22 HELIX 16 16 GLN A 425 LYS A 444 1 20 HELIX 17 17 LEU A 447 ILE A 455 5 9 HELIX 18 18 ARG A 460 GLU A 478 1 19 SHEET 1 A 6 ILE A 139 LYS A 140 0 SHEET 2 A 6 ILE A 160 VAL A 162 1 O MET A 161 N ILE A 139 SHEET 3 A 6 THR A 345 VAL A 348 -1 O THR A 345 N VAL A 162 SHEET 4 A 6 SER A 289 ILE A 304 -1 N TYR A 292 O LEU A 346 SHEET 5 A 6 ILE A 353 PHE A 369 -1 O PHE A 365 N HIS A 293 SHEET 6 A 6 TYR A 278 HIS A 282 -1 N THR A 279 O VAL A 356 SHEET 1 B 7 ASP A 202 THR A 206 0 SHEET 2 B 7 VAL A 191 ASP A 196 -1 N ILE A 192 O MET A 205 SHEET 3 B 7 LEU A 223 GLU A 229 -1 O ASN A 224 N ILE A 195 SHEET 4 B 7 TYR A 269 GLY A 273 -1 O CYS A 270 N LEU A 228 SHEET 5 B 7 ILE A 353 PHE A 369 -1 O ALA A 364 N LEU A 271 SHEET 6 B 7 SER A 289 ILE A 304 -1 N HIS A 293 O PHE A 365 SHEET 7 B 7 TYR A 336 VAL A 340 -1 O VAL A 340 N LYS A 299 LINK NE2 HIS A 282 NI NI A 489 1555 1555 2.48 LINK OD1 ASP A 284 NI NI A 489 1555 1555 2.37 LINK NE2 HIS A 354 NI NI A 489 1555 1555 2.36 LINK NI NI A 489 O2' OGA A5798 1555 1555 1.93 LINK NI NI A 489 O2 OGA A5798 1555 1555 2.04 SITE 1 AC1 4 HIS A 282 ASP A 284 HIS A 354 OGA A5798 SITE 1 AC2 5 SER A 249 TRP A 250 VAL A 251 PHE A 369 SITE 2 AC2 5 LEU A 370 SITE 1 AC3 2 VAL A 290 ASN A 368 SITE 1 AC4 10 ASN A 224 ILE A 226 THR A 279 HIS A 282 SITE 2 AC4 10 ASP A 284 TYR A 292 LYS A 299 HIS A 354 SITE 3 AC4 10 VAL A 356 NI A 489 CRYST1 78.300 78.300 289.100 90.00 90.00 120.00 P 61 2 2 12 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 0.012771 0.007374 0.000000 0.00000 SCALE2 0.000000 0.014747 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003459 0.00000