HEADER OXIDOREDUCTASE 24-APR-18 6GDY TITLE CRYSTAL STRUCTURE OF 2OG OXYGENASE JMJD6 (AA 1-343) IN COMPLEX WITH TITLE 2 FE(II) AND 2OG COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL ARGININE DEMETHYLASE AND LYSYL-HYDROXYLASE COMPND 3 JMJD6; COMPND 4 CHAIN: A, B; COMPND 5 SYNONYM: HISTONE ARGININE DEMETHYLASE JMJD6,JMJC DOMAIN-CONTAINING COMPND 6 PROTEIN 6,JUMONJI DOMAIN-CONTAINING PROTEIN 6,LYSYL-HYDROXYLASE COMPND 7 JMJD6,PEPTIDE-LYSINE 5-DIOXYGENASE JMJD6,PHOSPHATIDYLSERINE RECEPTOR, COMPND 8 PROTEIN PTDSR; COMPND 9 EC: 1.14.11.-; COMPND 10 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: JMJD6, KIAA0585, PTDSR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BI-FUNCTIONAL 2OG OXYGENASE, LYSYL HYDROXYLASE, ARGININE DEMETHYLASE, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.S.ISLAM,C.J.SCHOFIELD,M.A.MCDONOUGH REVDAT 2 16-OCT-19 6GDY 1 JRNL REVDAT 1 03-APR-19 6GDY 0 JRNL AUTH M.S.ISLAM,M.A.MCDONOUGH,R.CHOWDHURY,J.GAULT,A.KHAN,E.PIRES, JRNL AUTH 2 C.J.SCHOFIELD JRNL TITL BIOCHEMICAL AND STRUCTURAL INVESTIGATIONS CLARIFY THE JRNL TITL 2 SUBSTRATE SELECTIVITY OF THE 2-OXOGLUTARATE OXYGENASE JMJD6. JRNL REF J.BIOL.CHEM. V. 294 11637 2019 JRNL REFN ESSN 1083-351X JRNL PMID 31147442 JRNL DOI 10.1074/JBC.RA119.008693 REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_2906: ???) 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) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.23 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 53217 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.850 REMARK 3 FREE R VALUE TEST SET COUNT : 2580 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 42.2356 - 5.3430 0.99 2865 140 0.1920 0.1988 REMARK 3 2 5.3430 - 4.2422 0.99 2832 133 0.1306 0.1500 REMARK 3 3 4.2422 - 3.7063 1.00 2830 144 0.1318 0.1968 REMARK 3 4 3.7063 - 3.3676 1.00 2797 144 0.1484 0.1913 REMARK 3 5 3.3676 - 3.1263 1.00 2832 169 0.1685 0.2145 REMARK 3 6 3.1263 - 2.9420 1.00 2803 137 0.1777 0.2213 REMARK 3 7 2.9420 - 2.7947 1.00 2833 143 0.1835 0.2036 REMARK 3 8 2.7947 - 2.6731 1.00 2837 158 0.1959 0.2389 REMARK 3 9 2.6731 - 2.5702 1.00 2826 120 0.2038 0.2272 REMARK 3 10 2.5702 - 2.4815 1.00 2777 148 0.2034 0.2553 REMARK 3 11 2.4815 - 2.4039 1.00 2831 140 0.2100 0.2183 REMARK 3 12 2.4039 - 2.3352 1.00 2779 173 0.2090 0.2629 REMARK 3 13 2.3352 - 2.2738 1.00 2838 130 0.2295 0.2825 REMARK 3 14 2.2738 - 2.2183 1.00 2779 150 0.2361 0.2989 REMARK 3 15 2.2183 - 2.1679 1.00 2817 136 0.2411 0.2587 REMARK 3 16 2.1679 - 2.1217 0.99 2783 127 0.2550 0.2867 REMARK 3 17 2.1217 - 2.0793 0.99 2812 145 0.2691 0.2876 REMARK 3 18 2.0793 - 2.0400 0.99 2766 143 0.2916 0.3656 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.070 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.36 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 5680 REMARK 3 ANGLE : 0.583 7738 REMARK 3 CHIRALITY : 0.041 793 REMARK 3 PLANARITY : 0.003 986 REMARK 3 DIHEDRAL : 9.651 3355 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 6GDY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-APR-18. REMARK 100 THE DEPOSITION ID IS D_1200009766. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.07206 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53266 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 42.227 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 9.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 1.29700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: P1 21 1 REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 7.8, 0.7M NAH2PO4, 0.9M REMARK 280 KH2PO4, 3% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 48.49500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: 6840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -103.0 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 SER A 335 REMARK 465 THR A 336 REMARK 465 GLY A 337 REMARK 465 ILE A 338 REMARK 465 ALA A 339 REMARK 465 SER A 340 REMARK 465 ASP A 341 REMARK 465 SER A 342 REMARK 465 SER A 343 REMARK 465 SER B 335 REMARK 465 THR B 336 REMARK 465 GLY B 337 REMARK 465 ILE B 338 REMARK 465 ALA B 339 REMARK 465 SER B 340 REMARK 465 ASP B 341 REMARK 465 SER B 342 REMARK 465 SER B 343 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 4 CE NZ REMARK 470 LYS A 6 CE NZ REMARK 470 LYS A 7 NZ REMARK 470 ARG A 14 CD NE CZ NH1 NH2 REMARK 470 LEU A 24 CD1 CD2 REMARK 470 GLU A 33 CD OE1 OE2 REMARK 470 GLN A 53 CD OE1 NE2 REMARK 470 GLU A 61 CD OE1 OE2 REMARK 470 GLU A 83 CG CD OE1 OE2 REMARK 470 LYS A 98 NZ REMARK 470 GLU A 103 OE1 OE2 REMARK 470 LYS A 111 CE NZ REMARK 470 LYS A 142 CG CD CE NZ REMARK 470 ARG A 144 CZ NH1 NH2 REMARK 470 LYS A 145 CE NZ REMARK 470 GLU A 166 CG CD OE1 OE2 REMARK 470 LYS A 167 CG CD CE NZ REMARK 470 ARG A 168 CD NE CZ NH1 NH2 REMARK 470 ARG A 215 NE CZ NH1 NH2 REMARK 470 GLU A 216 CG CD OE1 OE2 REMARK 470 LYS A 253 CD CE NZ REMARK 470 LYS A 260 NZ REMARK 470 ARG A 303 CZ NH1 NH2 REMARK 470 LYS A 307 CD CE NZ REMARK 470 LYS A 311 CD CE NZ REMARK 470 ARG A 314 CD NE CZ NH1 NH2 REMARK 470 GLU A 334 CA C O CB CG CD OE1 REMARK 470 GLU A 334 OE2 REMARK 470 LYS B 4 CD CE NZ REMARK 470 LYS B 6 CE NZ REMARK 470 LYS B 7 CG CD CE NZ REMARK 470 ARG B 14 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 21 CE NZ REMARK 470 SER B 23 OG REMARK 470 LEU B 24 CG CD1 CD2 REMARK 470 ARG B 28 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 33 CD OE1 OE2 REMARK 470 GLN B 53 OE1 NE2 REMARK 470 GLU B 57 CG CD OE1 OE2 REMARK 470 GLU B 61 CD OE1 OE2 REMARK 470 GLU B 83 CG CD OE1 OE2 REMARK 470 LYS B 98 NZ REMARK 470 GLU B 103 CD OE1 OE2 REMARK 470 ASP B 106 OD1 OD2 REMARK 470 TYR B 108 CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS B 111 NZ REMARK 470 GLU B 122 OE1 OE2 REMARK 470 LYS B 142 CD CE NZ REMARK 470 ARG B 144 CZ NH1 NH2 REMARK 470 LYS B 145 CE NZ REMARK 470 GLU B 166 CG CD OE1 OE2 REMARK 470 LYS B 167 CD CE NZ REMARK 470 ARG B 168 CD NE CZ NH1 NH2 REMARK 470 ARG B 215 CZ NH1 NH2 REMARK 470 ARG B 222 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 253 CE NZ REMARK 470 LYS B 307 CG CD CE NZ REMARK 470 LYS B 311 CD CE NZ REMARK 470 ARG B 314 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 317 CG CD CE NZ 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 45 29.43 -140.83 REMARK 500 TYR A 63 -48.23 -132.01 REMARK 500 PHE A 133 76.53 -150.18 REMARK 500 LYS A 142 -59.02 80.02 REMARK 500 TYR A 172 -12.86 -140.93 REMARK 500 ARG A 181 -8.94 82.56 REMARK 500 ASP A 279 -163.30 -164.73 REMARK 500 TYR B 63 -50.67 -130.72 REMARK 500 PHE B 133 74.12 -150.92 REMARK 500 TYR B 172 -15.86 -141.29 REMARK 500 ARG B 181 -9.70 83.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 746 DISTANCE = 7.01 ANGSTROMS 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 FE A 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 187 NE2 REMARK 620 2 ASP A 189 OD1 81.8 REMARK 620 3 HIS A 273 NE2 76.2 81.7 REMARK 620 4 AKG A 402 O5 91.6 170.0 104.1 REMARK 620 5 AKG A 402 O2 93.3 99.8 169.0 72.9 REMARK 620 6 HOH A 682 O 171.1 93.6 95.7 93.9 95.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 187 NE2 REMARK 620 2 ASP B 189 OD1 101.0 REMARK 620 3 HIS B 273 NE2 80.1 88.0 REMARK 620 4 AKG B 402 O5 90.7 168.1 95.7 REMARK 620 5 AKG B 402 O1 99.4 101.0 170.9 75.2 REMARK 620 6 HOH B 542 O 165.9 85.9 87.9 83.0 91.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AKG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AKG B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 409 DBREF 6GDY A 1 343 UNP Q6NYC1 JMJD6_HUMAN 1 343 DBREF 6GDY B 1 343 UNP Q6NYC1 JMJD6_HUMAN 1 343 SEQRES 1 A 343 MET ASN HIS LYS SER LYS LYS ARG ILE ARG GLU ALA LYS SEQRES 2 A 343 ARG SER ALA ARG PRO GLU LEU LYS ASP SER LEU ASP TRP SEQRES 3 A 343 THR ARG HIS ASN TYR TYR GLU SER PHE SER LEU SER PRO SEQRES 4 A 343 ALA ALA VAL ALA ASP ASN VAL GLU ARG ALA ASP ALA LEU SEQRES 5 A 343 GLN LEU SER VAL GLU GLU PHE VAL GLU ARG TYR GLU ARG SEQRES 6 A 343 PRO TYR LYS PRO VAL VAL LEU LEU ASN ALA GLN GLU GLY SEQRES 7 A 343 TRP SER ALA GLN GLU LYS TRP THR LEU GLU ARG LEU LYS SEQRES 8 A 343 ARG LYS TYR ARG ASN GLN LYS PHE LYS CYS GLY GLU ASP SEQRES 9 A 343 ASN ASP GLY TYR SER VAL LYS MET LYS MET LYS TYR TYR SEQRES 10 A 343 ILE GLU TYR MET GLU SER THR ARG ASP ASP SER PRO LEU SEQRES 11 A 343 TYR ILE PHE ASP SER SER TYR GLY GLU HIS PRO LYS ARG SEQRES 12 A 343 ARG LYS LEU LEU GLU ASP TYR LYS VAL PRO LYS PHE PHE SEQRES 13 A 343 THR ASP ASP LEU PHE GLN TYR ALA GLY GLU LYS ARG ARG SEQRES 14 A 343 PRO PRO TYR ARG TRP PHE VAL MET GLY PRO PRO ARG SER SEQRES 15 A 343 GLY THR GLY ILE HIS ILE ASP PRO LEU GLY THR SER ALA SEQRES 16 A 343 TRP ASN ALA LEU VAL GLN GLY HIS LYS ARG TRP CYS LEU SEQRES 17 A 343 PHE PRO THR SER THR PRO ARG GLU LEU ILE LYS VAL THR SEQRES 18 A 343 ARG ASP GLU GLY GLY ASN GLN GLN ASP GLU ALA ILE THR SEQRES 19 A 343 TRP PHE ASN VAL ILE TYR PRO ARG THR GLN LEU PRO THR SEQRES 20 A 343 TRP PRO PRO GLU PHE LYS PRO LEU GLU ILE LEU GLN LYS SEQRES 21 A 343 PRO GLY GLU THR VAL PHE VAL PRO GLY GLY TRP TRP HIS SEQRES 22 A 343 VAL VAL LEU ASN LEU ASP THR THR ILE ALA ILE THR GLN SEQRES 23 A 343 ASN PHE ALA SER SER THR ASN PHE PRO VAL VAL TRP HIS SEQRES 24 A 343 LYS THR VAL ARG GLY ARG PRO LYS LEU SER ARG LYS TRP SEQRES 25 A 343 TYR ARG ILE LEU LYS GLN GLU HIS PRO GLU LEU ALA VAL SEQRES 26 A 343 LEU ALA ASP SER VAL ASP LEU GLN GLU SER THR GLY ILE SEQRES 27 A 343 ALA SER ASP SER SER SEQRES 1 B 343 MET ASN HIS LYS SER LYS LYS ARG ILE ARG GLU ALA LYS SEQRES 2 B 343 ARG SER ALA ARG PRO GLU LEU LYS ASP SER LEU ASP TRP SEQRES 3 B 343 THR ARG HIS ASN TYR TYR GLU SER PHE SER LEU SER PRO SEQRES 4 B 343 ALA ALA VAL ALA ASP ASN VAL GLU ARG ALA ASP ALA LEU SEQRES 5 B 343 GLN LEU SER VAL GLU GLU PHE VAL GLU ARG TYR GLU ARG SEQRES 6 B 343 PRO TYR LYS PRO VAL VAL LEU LEU ASN ALA GLN GLU GLY SEQRES 7 B 343 TRP SER ALA GLN GLU LYS TRP THR LEU GLU ARG LEU LYS SEQRES 8 B 343 ARG LYS TYR ARG ASN GLN LYS PHE LYS CYS GLY GLU ASP SEQRES 9 B 343 ASN ASP GLY TYR SER VAL LYS MET LYS MET LYS TYR TYR SEQRES 10 B 343 ILE GLU TYR MET GLU SER THR ARG ASP ASP SER PRO LEU SEQRES 11 B 343 TYR ILE PHE ASP SER SER TYR GLY GLU HIS PRO LYS ARG SEQRES 12 B 343 ARG LYS LEU LEU GLU ASP TYR LYS VAL PRO LYS PHE PHE SEQRES 13 B 343 THR ASP ASP LEU PHE GLN TYR ALA GLY GLU LYS ARG ARG SEQRES 14 B 343 PRO PRO TYR ARG TRP PHE VAL MET GLY PRO PRO ARG SER SEQRES 15 B 343 GLY THR GLY ILE HIS ILE ASP PRO LEU GLY THR SER ALA SEQRES 16 B 343 TRP ASN ALA LEU VAL GLN GLY HIS LYS ARG TRP CYS LEU SEQRES 17 B 343 PHE PRO THR SER THR PRO ARG GLU LEU ILE LYS VAL THR SEQRES 18 B 343 ARG ASP GLU GLY GLY ASN GLN GLN ASP GLU ALA ILE THR SEQRES 19 B 343 TRP PHE ASN VAL ILE TYR PRO ARG THR GLN LEU PRO THR SEQRES 20 B 343 TRP PRO PRO GLU PHE LYS PRO LEU GLU ILE LEU GLN LYS SEQRES 21 B 343 PRO GLY GLU THR VAL PHE VAL PRO GLY GLY TRP TRP HIS SEQRES 22 B 343 VAL VAL LEU ASN LEU ASP THR THR ILE ALA ILE THR GLN SEQRES 23 B 343 ASN PHE ALA SER SER THR ASN PHE PRO VAL VAL TRP HIS SEQRES 24 B 343 LYS THR VAL ARG GLY ARG PRO LYS LEU SER ARG LYS TRP SEQRES 25 B 343 TYR ARG ILE LEU LYS GLN GLU HIS PRO GLU LEU ALA VAL SEQRES 26 B 343 LEU ALA ASP SER VAL ASP LEU GLN GLU SER THR GLY ILE SEQRES 27 B 343 ALA SER ASP SER SER HET FE A 401 1 HET AKG A 402 10 HET NA A 403 1 HET PO4 A 404 5 HET PO4 A 405 5 HET PO4 A 406 5 HET PO4 A 407 5 HET PO4 A 408 5 HET EPE A 409 15 HET EPE A 410 15 HET GOL A 411 6 HET FE B 401 1 HET AKG B 402 10 HET PO4 B 403 5 HET PO4 B 404 5 HET PO4 B 405 5 HET PO4 B 406 5 HET PO4 B 407 5 HET GOL B 408 6 HET GOL B 409 6 HETNAM FE FE (III) ION HETNAM AKG 2-OXOGLUTARIC ACID HETNAM NA SODIUM ION HETNAM PO4 PHOSPHATE ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM GOL GLYCEROL HETSYN EPE HEPES HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 FE 2(FE 3+) FORMUL 4 AKG 2(C5 H6 O5) FORMUL 5 NA NA 1+ FORMUL 6 PO4 10(O4 P 3-) FORMUL 11 EPE 2(C8 H18 N2 O4 S) FORMUL 13 GOL 3(C3 H8 O3) FORMUL 23 HOH *455(H2 O) HELIX 1 AA1 ASN A 2 ARG A 17 1 16 HELIX 2 AA2 ASP A 22 ARG A 28 1 7 HELIX 3 AA3 ASN A 30 PHE A 35 1 6 HELIX 4 AA4 SER A 38 VAL A 42 5 5 HELIX 5 AA5 LEU A 52 LEU A 54 5 3 HELIX 6 AA6 SER A 55 TYR A 63 1 9 HELIX 7 AA7 SER A 80 TRP A 85 1 6 HELIX 8 AA8 THR A 86 TYR A 94 1 9 HELIX 9 AA9 MET A 114 GLU A 122 1 9 HELIX 10 AB1 SER A 136 HIS A 140 5 5 HELIX 11 AB2 LYS A 142 TYR A 150 5 9 HELIX 12 AB3 PRO A 153 THR A 157 5 5 HELIX 13 AB4 ASP A 159 GLY A 165 5 7 HELIX 14 AB5 ASP A 189 THR A 193 5 5 HELIX 15 AB6 PRO A 214 LYS A 219 1 6 HELIX 16 AB7 THR A 221 GLY A 226 1 6 HELIX 17 AB8 ASN A 227 GLN A 229 5 3 HELIX 18 AB9 GLU A 231 ILE A 239 1 9 HELIX 19 AC1 ILE A 239 GLN A 244 1 6 HELIX 20 AC2 PRO A 249 LYS A 253 5 5 HELIX 21 AC3 ASN A 293 ARG A 305 1 13 HELIX 22 AC4 ARG A 305 HIS A 320 1 16 HELIX 23 AC5 HIS A 320 GLN A 333 1 14 HELIX 24 AC6 ASN B 2 ARG B 17 1 16 HELIX 25 AC7 ASP B 22 ARG B 28 1 7 HELIX 26 AC8 ASN B 30 PHE B 35 1 6 HELIX 27 AC9 SER B 38 VAL B 42 5 5 HELIX 28 AD1 LEU B 52 LEU B 54 5 3 HELIX 29 AD2 SER B 55 TYR B 63 1 9 HELIX 30 AD3 SER B 80 TRP B 85 1 6 HELIX 31 AD4 THR B 86 TYR B 94 1 9 HELIX 32 AD5 MET B 114 THR B 124 1 11 HELIX 33 AD6 SER B 136 HIS B 140 5 5 HELIX 34 AD7 LYS B 142 TYR B 150 5 9 HELIX 35 AD8 PRO B 153 THR B 157 5 5 HELIX 36 AD9 ASP B 159 GLY B 165 5 7 HELIX 37 AE1 ASP B 189 THR B 193 5 5 HELIX 38 AE2 PRO B 214 LYS B 219 1 6 HELIX 39 AE3 THR B 221 GLY B 226 1 6 HELIX 40 AE4 ASN B 227 GLN B 229 5 3 HELIX 41 AE5 GLU B 231 ILE B 239 1 9 HELIX 42 AE6 ILE B 239 GLN B 244 1 6 HELIX 43 AE7 PRO B 249 LYS B 253 5 5 HELIX 44 AE8 ASN B 293 ARG B 305 1 13 HELIX 45 AE9 ARG B 305 HIS B 320 1 16 HELIX 46 AF1 HIS B 320 GLU B 334 1 15 SHEET 1 AA1 7 ARG A 48 ASP A 50 0 SHEET 2 AA1 7 VAL A 70 LEU A 73 1 O LEU A 73 N ALA A 49 SHEET 3 AA1 7 THR A 264 VAL A 267 -1 O THR A 264 N LEU A 72 SHEET 4 AA1 7 SER A 194 GLN A 201 -1 N ALA A 195 O VAL A 267 SHEET 5 AA1 7 THR A 281 PHE A 288 -1 O ILE A 284 N ALA A 198 SHEET 6 AA1 7 ARG A 173 GLY A 178 -1 N VAL A 176 O ALA A 283 SHEET 7 AA1 7 ILE A 132 ASP A 134 -1 N ASP A 134 O PHE A 175 SHEET 1 AA2 2 LYS A 98 GLU A 103 0 SHEET 2 AA2 2 SER A 109 LYS A 113 -1 O VAL A 110 N CYS A 101 SHEET 1 AA3 4 GLY A 183 HIS A 187 0 SHEET 2 AA3 4 TRP A 272 ASN A 277 -1 O HIS A 273 N HIS A 187 SHEET 3 AA3 4 LYS A 204 PHE A 209 -1 N ARG A 205 O LEU A 276 SHEET 4 AA3 4 LEU A 255 GLN A 259 -1 O GLN A 259 N LYS A 204 SHEET 1 AA4 7 ARG B 48 ASP B 50 0 SHEET 2 AA4 7 VAL B 70 LEU B 73 1 O LEU B 73 N ALA B 49 SHEET 3 AA4 7 THR B 264 VAL B 267 -1 O THR B 264 N LEU B 72 SHEET 4 AA4 7 SER B 194 GLN B 201 -1 N ALA B 195 O VAL B 267 SHEET 5 AA4 7 THR B 281 PHE B 288 -1 O ILE B 284 N ALA B 198 SHEET 6 AA4 7 ARG B 173 GLY B 178 -1 N VAL B 176 O ALA B 283 SHEET 7 AA4 7 ILE B 132 ASP B 134 -1 N ASP B 134 O PHE B 175 SHEET 1 AA5 2 LYS B 98 GLU B 103 0 SHEET 2 AA5 2 SER B 109 LYS B 113 -1 O VAL B 110 N CYS B 101 SHEET 1 AA6 4 GLY B 183 HIS B 187 0 SHEET 2 AA6 4 TRP B 272 ASN B 277 -1 O VAL B 275 N THR B 184 SHEET 3 AA6 4 LYS B 204 PHE B 209 -1 N ARG B 205 O LEU B 276 SHEET 4 AA6 4 LEU B 255 GLN B 259 -1 O GLN B 259 N LYS B 204 LINK NE2 HIS A 187 FE FE A 401 1555 1555 2.30 LINK OD1 ASP A 189 FE FE A 401 1555 1555 2.35 LINK NE2 HIS A 273 FE FE A 401 1555 1555 2.31 LINK NE2 HIS B 187 FE FE B 401 1555 1555 2.30 LINK OD1 ASP B 189 FE FE B 401 1555 1555 2.20 LINK NE2 HIS B 273 FE FE B 401 1555 1555 2.26 LINK FE FE A 401 O5 AKG A 402 1555 1555 2.21 LINK FE FE A 401 O2 AKG A 402 1555 1555 2.28 LINK FE FE A 401 O HOH A 682 1555 1555 2.28 LINK FE FE B 401 O5 AKG B 402 1555 1555 2.33 LINK FE FE B 401 O1 AKG B 402 1555 1555 2.22 LINK FE FE B 401 O HOH B 542 1555 1555 2.46 SITE 1 AC1 5 HIS A 187 ASP A 189 HIS A 273 AKG A 402 SITE 2 AC1 5 HOH A 682 SITE 1 AC2 12 TYR A 131 PHE A 133 THR A 184 HIS A 187 SITE 2 AC2 12 ASP A 189 ASN A 197 LYS A 204 HIS A 273 SITE 3 AC2 12 VAL A 275 FE A 401 HOH A 558 HOH A 598 SITE 1 AC3 2 THR A 86 LEU A 87 SITE 1 AC4 4 SER A 109 SER A 136 HOH A 531 HOH A 650 SITE 1 AC5 9 ALA A 75 GLN A 76 GLU A 77 TRP A 79 SITE 2 AC5 9 LYS A 151 PRO A 153 HOH A 511 HOH A 521 SITE 3 AC5 9 HOH A 572 SITE 1 AC6 4 ARG A 305 PRO A 306 LYS A 307 LEU A 308 SITE 1 AC7 4 LYS A 91 ARG A 95 GLU A 119 GLU B 88 SITE 1 AC8 6 LYS A 4 ARG A 8 LYS A 113 TYR A 116 SITE 2 AC8 6 HOH A 501 HOH A 586 SITE 1 AC9 7 LYS A 84 ARG A 89 LYS A 93 HOH A 643 SITE 2 AC9 7 ARG B 95 ASN B 96 LYS B 115 SITE 1 AD1 7 ARG A 95 ASN A 96 LYS A 115 HOH A 679 SITE 2 AD1 7 LYS B 84 ARG B 89 LYS B 93 SITE 1 AD2 7 TYR A 67 THR A 211 GLY A 269 GLY A 270 SITE 2 AD2 7 HOH A 522 GLU B 61 ARG B 65 SITE 1 AD3 5 HIS B 187 ASP B 189 HIS B 273 AKG B 402 SITE 2 AD3 5 HOH B 542 SITE 1 AD4 12 TYR B 131 PHE B 133 THR B 184 HIS B 187 SITE 2 AD4 12 ASP B 189 ASN B 197 LYS B 204 HIS B 273 SITE 3 AD4 12 FE B 401 HOH B 507 HOH B 518 HOH B 613 SITE 1 AD5 4 SER B 55 VAL B 56 LYS B 154 HOH B 501 SITE 1 AD6 4 SER B 109 LYS B 111 SER B 136 HOH B 650 SITE 1 AD7 4 ARG B 305 PRO B 306 LYS B 307 LEU B 308 SITE 1 AD8 5 ARG B 8 LYS B 113 TYR B 116 HOH B 528 SITE 2 AD8 5 HOH B 558 SITE 1 AD9 5 SER A 329 VAL A 330 GLN A 333 ARG B 65 SITE 2 AD9 5 SER B 291 SITE 1 AE1 7 ALA B 75 GLN B 76 GLU B 77 TRP B 79 SITE 2 AE1 7 LYS B 151 PRO B 153 LYS B 154 SITE 1 AE2 9 ARG B 17 TRP B 26 SER B 128 LEU B 130 SITE 2 AE2 9 GLY B 183 GLU B 231 HOH B 516 HOH B 566 SITE 3 AE2 9 HOH B 699 CRYST1 47.150 96.990 93.760 90.00 95.84 90.00 P 1 21 1 4 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 0.021209 0.000000 0.002169 0.00000 SCALE2 0.000000 0.010310 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010721 0.00000