HEADER OXIDOREDUCTASE 30-SEP-09 3K2O TITLE STRUCTURE OF AN OXYGENASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL ARGININE DEMETHYLASE AND LYSYL-HYDROXYLASE COMPND 3 JMJD6; COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: UNP RESIDUES 2-335; COMPND 6 SYNONYM: HISTONE ARGININE DEMETHYLASE JMJD6, PEPTIDE-LYSINE 5- COMPND 7 DIOXYGENASE JMJD6, LYSYL-HYDROXYLASE JMJD6, JMJC DOMAIN-CONTAINING COMPND 8 PROTEIN 6, JUMONJI DOMAIN-CONTAINING PROTEIN 6, PHOSPHATIDYLSERINE COMPND 9 RECEPTOR, PROTEIN PTDSR; COMPND 10 EC: 1.14.11.-; COMPND 11 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 STRUCTURAL GENOMICS CONSORTIUM, SGC, CHROMATIN REGULATOR, KEYWDS 2 DEVELOPMENTAL PROTEIN, DIFFERENTIATION, DIOXYGENASE, IRON, METAL- KEYWDS 3 BINDING, MRNA PROCESSING, MRNA SPLICING, NUCLEUS, OXIDOREDUCTASE, KEYWDS 4 TRANSCRIPTION, TRANSCRIPTION REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR T.KROJER,M.A.MCDONOUGH,I.J.CLIFTON,M.MANTRI,S.S.NG,A.C.W.PIKE, AUTHOR 2 D.S.BUTLER,C.J.WEBBY,G.KOCHAN,C.BHATIA,J.E.BRAY,A.CHAIKUAD, AUTHOR 3 O.GILEADI,F.VON DELFT,J.WEIGELT,C.H.ARROWSMITH,C.BOUNTRA, AUTHOR 4 A.M.EDWARDS,C.J.SCHOFIELD,K.L.KAVANAGH,U.OPPERMANN REVDAT 4 13-JUL-11 3K2O 1 VERSN REVDAT 3 15-SEP-10 3K2O 1 JRNL REVDAT 2 09-JUN-10 3K2O 1 JRNL REVDAT 1 03-NOV-09 3K2O 0 JRNL AUTH M.MANTRI,T.KROJER,E.A.BAGG,C.A.WEBBY,D.S.BUTLER,G.KOCHAN, JRNL AUTH 2 K.L.KAVANAGH,U.OPPERMANN,M.A.MCDONOUGH,C.J.SCHOFIELD JRNL TITL CRYSTAL STRUCTURE OF THE 2-OXOGLUTARATE- AND JRNL TITL 2 FE(II)-DEPENDENT LYSYL HYDROXYLASE JMJD6. JRNL REF J.MOL.BIOL. V. 401 211 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20685276 JRNL DOI 10.1016/J.JMB.2010.05.054 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.4_162) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 95145 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4855 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 19.8520 - 5.4021 0.89 2796 167 0.2157 0.2213 REMARK 3 2 5.4021 - 4.3022 0.95 2952 162 0.1383 0.1649 REMARK 3 3 4.3022 - 3.7625 0.96 2959 147 0.1482 0.1752 REMARK 3 4 3.7625 - 3.4204 0.97 3025 160 0.1693 0.1991 REMARK 3 5 3.4204 - 3.1763 0.97 3000 158 0.1821 0.2215 REMARK 3 6 3.1763 - 2.9897 0.97 2995 159 0.1838 0.2240 REMARK 3 7 2.9897 - 2.8405 0.98 3045 149 0.1908 0.2172 REMARK 3 8 2.8405 - 2.7171 0.98 3025 156 0.1914 0.2496 REMARK 3 9 2.7171 - 2.6128 0.98 2977 190 0.1891 0.2339 REMARK 3 10 2.6128 - 2.5228 0.98 3041 144 0.1902 0.2596 REMARK 3 11 2.5228 - 2.4441 0.98 2989 185 0.1872 0.2271 REMARK 3 12 2.4441 - 2.3743 0.98 3049 175 0.1816 0.2197 REMARK 3 13 2.3743 - 2.3119 0.98 3068 132 0.1845 0.2135 REMARK 3 14 2.3119 - 2.2556 0.98 2982 159 0.1843 0.2074 REMARK 3 15 2.2556 - 2.2044 0.98 3084 158 0.1853 0.2296 REMARK 3 16 2.2044 - 2.1575 0.99 2980 167 0.1857 0.2479 REMARK 3 17 2.1575 - 2.1144 0.98 3087 139 0.1892 0.2152 REMARK 3 18 2.1144 - 2.0745 0.98 2995 163 0.1879 0.2377 REMARK 3 19 2.0745 - 2.0375 0.98 3024 160 0.1937 0.2377 REMARK 3 20 2.0375 - 2.0030 0.98 3033 169 0.1991 0.2152 REMARK 3 21 2.0030 - 1.9707 0.99 2998 186 0.1970 0.2489 REMARK 3 22 1.9707 - 1.9404 0.99 3040 167 0.2259 0.2546 REMARK 3 23 1.9404 - 1.9119 0.98 2999 183 0.2329 0.2674 REMARK 3 24 1.9119 - 1.8850 0.98 3012 155 0.2410 0.2852 REMARK 3 25 1.8850 - 1.8596 0.98 3035 164 0.2408 0.2882 REMARK 3 26 1.8596 - 1.8354 0.98 2992 172 0.2475 0.2984 REMARK 3 27 1.8354 - 1.8125 0.98 3061 145 0.2560 0.2871 REMARK 3 28 1.8125 - 1.7907 0.98 3007 174 0.2650 0.2838 REMARK 3 29 1.7907 - 1.7699 0.98 2990 164 0.2772 0.2853 REMARK 3 30 1.7699 - 1.7500 0.98 3050 146 0.2856 0.3220 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : 0.39 REMARK 3 B_SOL : 69.19 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.920 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.01890 REMARK 3 B22 (A**2) : 3.86830 REMARK 3 B33 (A**2) : -4.88720 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.46660 REMARK 3 B23 (A**2) : 0.00000 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 : 0.017 5858 REMARK 3 ANGLE : 1.386 7967 REMARK 3 CHIRALITY : 0.096 809 REMARK 3 PLANARITY : 0.005 1028 REMARK 3 DIHEDRAL : 15.469 2184 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 6.5805 22.1674 48.7935 REMARK 3 T TENSOR REMARK 3 T11: 0.0340 T22: 0.0371 REMARK 3 T33: 0.0547 T12: -0.0035 REMARK 3 T13: -0.0036 T23: -0.0145 REMARK 3 L TENSOR REMARK 3 L11: 0.4724 L22: 0.0800 REMARK 3 L33: 0.7075 L12: 0.0341 REMARK 3 L13: -0.3313 L23: 0.0500 REMARK 3 S TENSOR REMARK 3 S11: 0.0174 S12: 0.0028 S13: 0.0240 REMARK 3 S21: 0.0041 S22: -0.0089 S23: 0.0074 REMARK 3 S31: 0.0163 S32: -0.0159 S33: -0.0046 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 3K2O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-OCT-09. REMARK 100 THE RCSB ID CODE IS RCSB055469. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 95190 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 148.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : 0.05200 REMARK 200 FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.43700 REMARK 200 R SYM FOR SHELL (I) : 0.43700 REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.8M NAH2PO4, 0.8M KH2PO4, 0.1M REMARK 280 NAHEPES 7.5, VAPOR DIFFUSION, TEMPERATURE 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 51.01500 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: 2050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 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 HIS A 0 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 57 CG CD OE1 OE2 REMARK 470 LYS A 307 CG CD CE NZ REMARK 470 LYS A 311 CG CD CE NZ REMARK 470 GLU A 334 CG CD OE1 OE2 REMARK 470 HIS B 0 CG ND1 CD2 CE1 NE2 REMARK 470 GLU B 57 CG CD OE1 OE2 REMARK 470 LYS B 307 CG CD CE NZ REMARK 470 LYS B 311 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 TYR A 63 -50.97 -127.75 REMARK 500 TYR A 172 -12.29 -151.67 REMARK 500 ARG A 181 -15.47 84.29 REMARK 500 TYR B 172 -12.88 -150.07 REMARK 500 ARG B 181 -13.05 85.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 THR B 157 24.9 L L OUTSIDE RANGE 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 369 DISTANCE = 5.02 ANGSTROMS REMARK 525 HOH A 500 DISTANCE = 5.55 ANGSTROMS REMARK 525 HOH A 597 DISTANCE = 5.24 ANGSTROMS REMARK 525 HOH A 613 DISTANCE = 5.08 ANGSTROMS REMARK 525 HOH A 688 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH A 691 DISTANCE = 5.63 ANGSTROMS REMARK 525 HOH A 702 DISTANCE = 5.74 ANGSTROMS REMARK 525 HOH B 386 DISTANCE = 5.16 ANGSTROMS REMARK 525 HOH B 451 DISTANCE = 5.18 ANGSTROMS REMARK 525 HOH B 644 DISTANCE = 5.30 ANGSTROMS REMARK 525 HOH B 663 DISTANCE = 5.30 ANGSTROMS REMARK 525 HOH B 694 DISTANCE = 6.30 ANGSTROMS REMARK 525 HOH B 704 DISTANCE = 5.58 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 NI A 336 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 187 NE2 REMARK 620 2 ASP A 189 OD1 94.4 REMARK 620 3 HIS A 273 NE2 90.1 96.8 REMARK 620 4 HOH A 715 O 89.5 170.9 91.4 REMARK 620 5 HOH A 717 O 89.7 80.7 177.5 91.1 REMARK 620 6 HOH A 716 O 176.7 88.1 91.7 87.8 88.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 336 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 187 NE2 REMARK 620 2 ASP B 189 OD1 94.3 REMARK 620 3 HIS B 273 NE2 90.2 97.3 REMARK 620 4 HOH B 356 O 171.7 86.9 97.8 REMARK 620 5 HOH B 346 O 86.1 79.8 175.1 86.0 REMARK 620 6 HOH B 354 O 90.5 166.6 95.2 86.7 88.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 341 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE B 155 O REMARK 620 2 HOH B 398 O 55.0 REMARK 620 N 1 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 336 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 337 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 338 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 339 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 340 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 341 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 336 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 337 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 338 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 339 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 340 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 341 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 342 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 343 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 344 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 345 DBREF 3K2O A 2 335 UNP Q6NYC1 JMJD6_HUMAN 2 335 DBREF 3K2O B 2 335 UNP Q6NYC1 JMJD6_HUMAN 2 335 SEQADV 3K2O HIS A 0 UNP Q6NYC1 EXPRESSION TAG SEQADV 3K2O MSE A 1 UNP Q6NYC1 EXPRESSION TAG SEQADV 3K2O HIS B 0 UNP Q6NYC1 EXPRESSION TAG SEQADV 3K2O MSE B 1 UNP Q6NYC1 EXPRESSION TAG SEQRES 1 A 336 HIS MSE ASN HIS LYS SER LYS LYS ARG ILE ARG GLU ALA SEQRES 2 A 336 LYS ARG SER ALA ARG PRO GLU LEU LYS ASP SER LEU ASP SEQRES 3 A 336 TRP THR ARG HIS ASN TYR TYR GLU SER PHE SER LEU SER SEQRES 4 A 336 PRO ALA ALA VAL ALA ASP ASN VAL GLU ARG ALA ASP ALA SEQRES 5 A 336 LEU GLN LEU SER VAL GLU GLU PHE VAL GLU ARG TYR GLU SEQRES 6 A 336 ARG PRO TYR LYS PRO VAL VAL LEU LEU ASN ALA GLN GLU SEQRES 7 A 336 GLY TRP SER ALA GLN GLU LYS TRP THR LEU GLU ARG LEU SEQRES 8 A 336 LYS ARG LYS TYR ARG ASN GLN LYS PHE LYS CYS GLY GLU SEQRES 9 A 336 ASP ASN ASP GLY TYR SER VAL LYS MSE LYS MSE LYS TYR SEQRES 10 A 336 TYR ILE GLU TYR MSE GLU SER THR ARG ASP ASP SER PRO SEQRES 11 A 336 LEU TYR ILE PHE ASP SER SER TYR GLY GLU HIS PRO LYS SEQRES 12 A 336 ARG ARG LYS LEU LEU GLU ASP TYR LYS VAL PRO LYS PHE SEQRES 13 A 336 PHE THR ASP ASP LEU PHE GLN TYR ALA GLY GLU LYS ARG SEQRES 14 A 336 ARG PRO PRO TYR ARG TRP PHE VAL MSE GLY PRO PRO ARG SEQRES 15 A 336 SER GLY THR GLY ILE HIS ILE ASP PRO LEU GLY THR SER SEQRES 16 A 336 ALA TRP ASN ALA LEU VAL GLN GLY HIS LYS ARG TRP CYS SEQRES 17 A 336 LEU PHE PRO THR SER THR PRO ARG GLU LEU ILE LYS VAL SEQRES 18 A 336 THR ARG ASP GLU GLY GLY ASN GLN GLN ASP GLU ALA ILE SEQRES 19 A 336 THR TRP PHE ASN VAL ILE TYR PRO ARG THR GLN LEU PRO SEQRES 20 A 336 THR TRP PRO PRO GLU PHE LYS PRO LEU GLU ILE LEU GLN SEQRES 21 A 336 LYS PRO GLY GLU THR VAL PHE VAL PRO GLY GLY TRP TRP SEQRES 22 A 336 HIS VAL VAL LEU ASN LEU ASP THR THR ILE ALA ILE THR SEQRES 23 A 336 GLN ASN PHE ALA SER SER THR ASN PHE PRO VAL VAL TRP SEQRES 24 A 336 HIS LYS THR VAL ARG GLY ARG PRO LYS LEU SER ARG LYS SEQRES 25 A 336 TRP TYR ARG ILE LEU LYS GLN GLU HIS PRO GLU LEU ALA SEQRES 26 A 336 VAL LEU ALA ASP SER VAL ASP LEU GLN GLU SER SEQRES 1 B 336 HIS MSE ASN HIS LYS SER LYS LYS ARG ILE ARG GLU ALA SEQRES 2 B 336 LYS ARG SER ALA ARG PRO GLU LEU LYS ASP SER LEU ASP SEQRES 3 B 336 TRP THR ARG HIS ASN TYR TYR GLU SER PHE SER LEU SER SEQRES 4 B 336 PRO ALA ALA VAL ALA ASP ASN VAL GLU ARG ALA ASP ALA SEQRES 5 B 336 LEU GLN LEU SER VAL GLU GLU PHE VAL GLU ARG TYR GLU SEQRES 6 B 336 ARG PRO TYR LYS PRO VAL VAL LEU LEU ASN ALA GLN GLU SEQRES 7 B 336 GLY TRP SER ALA GLN GLU LYS TRP THR LEU GLU ARG LEU SEQRES 8 B 336 LYS ARG LYS TYR ARG ASN GLN LYS PHE LYS CYS GLY GLU SEQRES 9 B 336 ASP ASN ASP GLY TYR SER VAL LYS MSE LYS MSE LYS TYR SEQRES 10 B 336 TYR ILE GLU TYR MSE GLU SER THR ARG ASP ASP SER PRO SEQRES 11 B 336 LEU TYR ILE PHE ASP SER SER TYR GLY GLU HIS PRO LYS SEQRES 12 B 336 ARG ARG LYS LEU LEU GLU ASP TYR LYS VAL PRO LYS PHE SEQRES 13 B 336 PHE THR ASP ASP LEU PHE GLN TYR ALA GLY GLU LYS ARG SEQRES 14 B 336 ARG PRO PRO TYR ARG TRP PHE VAL MSE GLY PRO PRO ARG SEQRES 15 B 336 SER GLY THR GLY ILE HIS ILE ASP PRO LEU GLY THR SER SEQRES 16 B 336 ALA TRP ASN ALA LEU VAL GLN GLY HIS LYS ARG TRP CYS SEQRES 17 B 336 LEU PHE PRO THR SER THR PRO ARG GLU LEU ILE LYS VAL SEQRES 18 B 336 THR ARG ASP GLU GLY GLY ASN GLN GLN ASP GLU ALA ILE SEQRES 19 B 336 THR TRP PHE ASN VAL ILE TYR PRO ARG THR GLN LEU PRO SEQRES 20 B 336 THR TRP PRO PRO GLU PHE LYS PRO LEU GLU ILE LEU GLN SEQRES 21 B 336 LYS PRO GLY GLU THR VAL PHE VAL PRO GLY GLY TRP TRP SEQRES 22 B 336 HIS VAL VAL LEU ASN LEU ASP THR THR ILE ALA ILE THR SEQRES 23 B 336 GLN ASN PHE ALA SER SER THR ASN PHE PRO VAL VAL TRP SEQRES 24 B 336 HIS LYS THR VAL ARG GLY ARG PRO LYS LEU SER ARG LYS SEQRES 25 B 336 TRP TYR ARG ILE LEU LYS GLN GLU HIS PRO GLU LEU ALA SEQRES 26 B 336 VAL LEU ALA ASP SER VAL ASP LEU GLN GLU SER MODRES 3K2O MSE A 1 MET SELENOMETHIONINE MODRES 3K2O MSE A 112 MET SELENOMETHIONINE MODRES 3K2O MSE A 114 MET SELENOMETHIONINE MODRES 3K2O MSE A 121 MET SELENOMETHIONINE MODRES 3K2O MSE A 177 MET SELENOMETHIONINE MODRES 3K2O MSE B 1 MET SELENOMETHIONINE MODRES 3K2O MSE B 112 MET SELENOMETHIONINE MODRES 3K2O MSE B 114 MET SELENOMETHIONINE MODRES 3K2O MSE B 121 MET SELENOMETHIONINE MODRES 3K2O MSE B 177 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 112 8 HET MSE A 114 8 HET MSE A 121 8 HET MSE A 177 8 HET MSE B 1 8 HET MSE B 112 8 HET MSE B 114 8 HET MSE B 121 8 HET MSE B 177 8 HET NI A 336 1 HET NA A 337 1 HET CL A 338 1 HET PO4 A 339 5 HET ACT A 340 4 HET GOL A 341 6 HET NI B 336 1 HET CL B 337 1 HET PO4 B 338 5 HET CL B 339 1 HET CL B 340 1 HET NA B 341 1 HET CL B 342 1 HET CL B 343 1 HET PO4 B 344 5 HET ACT B 345 4 HETNAM MSE SELENOMETHIONINE HETNAM NI NICKEL (II) ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM PO4 PHOSPHATE ION HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 10(C5 H11 N O2 SE) FORMUL 3 NI 2(NI 2+) FORMUL 4 NA 2(NA 1+) FORMUL 5 CL 6(CL 1-) FORMUL 6 PO4 3(O4 P 3-) FORMUL 7 ACT 2(C2 H3 O2 1-) FORMUL 8 GOL C3 H8 O3 FORMUL 19 HOH *673(H2 O) HELIX 1 1 ASN A 2 ARG A 17 1 16 HELIX 2 2 ASP A 22 ARG A 28 1 7 HELIX 3 3 ASN A 30 PHE A 35 1 6 HELIX 4 4 SER A 38 VAL A 42 5 5 HELIX 5 5 LEU A 52 LEU A 54 5 3 HELIX 6 6 SER A 55 TYR A 63 1 9 HELIX 7 7 SER A 80 TRP A 85 1 6 HELIX 8 8 THR A 86 TYR A 94 1 9 HELIX 9 9 MSE A 114 THR A 124 1 11 HELIX 10 10 SER A 136 HIS A 140 5 5 HELIX 11 11 LYS A 142 TYR A 150 5 9 HELIX 12 12 PRO A 153 THR A 157 5 5 HELIX 13 13 ASP A 159 GLY A 165 5 7 HELIX 14 14 ASP A 189 THR A 193 5 5 HELIX 15 15 PRO A 214 LYS A 219 1 6 HELIX 16 16 THR A 221 GLY A 226 1 6 HELIX 17 17 ASN A 227 GLN A 229 5 3 HELIX 18 18 GLU A 231 ILE A 239 1 9 HELIX 19 19 TYR A 240 LEU A 245 5 6 HELIX 20 20 PRO A 249 LYS A 253 5 5 HELIX 21 21 ASN A 293 ARG A 305 1 13 HELIX 22 22 ARG A 305 HIS A 320 1 16 HELIX 23 23 HIS A 320 GLU A 334 1 15 HELIX 24 24 ASN B 2 ARG B 17 1 16 HELIX 25 25 ASP B 22 ARG B 28 1 7 HELIX 26 26 ASN B 30 PHE B 35 1 6 HELIX 27 27 SER B 38 VAL B 42 5 5 HELIX 28 28 LEU B 52 LEU B 54 5 3 HELIX 29 29 SER B 55 TYR B 63 1 9 HELIX 30 30 SER B 80 TRP B 85 1 6 HELIX 31 31 THR B 86 TYR B 94 1 9 HELIX 32 32 MSE B 114 GLU B 122 1 9 HELIX 33 33 SER B 136 HIS B 140 5 5 HELIX 34 34 LYS B 142 TYR B 150 5 9 HELIX 35 35 PRO B 153 THR B 157 5 5 HELIX 36 36 ASP B 159 GLY B 165 5 7 HELIX 37 37 ASP B 189 THR B 193 5 5 HELIX 38 38 PRO B 214 LYS B 219 1 6 HELIX 39 39 THR B 221 GLY B 226 1 6 HELIX 40 40 ASN B 227 GLN B 229 5 3 HELIX 41 41 GLU B 231 ILE B 239 1 9 HELIX 42 42 ILE B 239 GLN B 244 1 6 HELIX 43 43 PRO B 249 LYS B 253 5 5 HELIX 44 44 ASN B 293 ARG B 305 1 13 HELIX 45 45 ARG B 305 HIS B 320 1 16 HELIX 46 46 HIS B 320 GLU B 334 1 15 SHEET 1 A 7 ARG A 48 ASP A 50 0 SHEET 2 A 7 VAL A 70 LEU A 73 1 O LEU A 73 N ALA A 49 SHEET 3 A 7 THR A 264 VAL A 267 -1 O THR A 264 N LEU A 72 SHEET 4 A 7 SER A 194 GLN A 201 -1 N ALA A 195 O VAL A 267 SHEET 5 A 7 THR A 281 PHE A 288 -1 O ILE A 284 N ALA A 198 SHEET 6 A 7 ARG A 173 GLY A 178 -1 N VAL A 176 O ALA A 283 SHEET 7 A 7 ILE A 132 ASP A 134 -1 N ILE A 132 O MSE A 177 SHEET 1 B 2 LYS A 98 GLU A 103 0 SHEET 2 B 2 SER A 109 LYS A 113 -1 O VAL A 110 N CYS A 101 SHEET 1 C 4 GLY A 183 HIS A 187 0 SHEET 2 C 4 TRP A 272 ASN A 277 -1 O VAL A 275 N THR A 184 SHEET 3 C 4 LYS A 204 PHE A 209 -1 N ARG A 205 O LEU A 276 SHEET 4 C 4 LEU A 255 GLN A 259 -1 O GLN A 259 N LYS A 204 SHEET 1 D 7 ARG B 48 ASP B 50 0 SHEET 2 D 7 VAL B 70 LEU B 73 1 O LEU B 73 N ALA B 49 SHEET 3 D 7 THR B 264 VAL B 267 -1 O THR B 264 N LEU B 72 SHEET 4 D 7 SER B 194 GLN B 201 -1 N ALA B 195 O VAL B 267 SHEET 5 D 7 THR B 281 PHE B 288 -1 O ILE B 284 N ALA B 198 SHEET 6 D 7 ARG B 173 GLY B 178 -1 N GLY B 178 O THR B 281 SHEET 7 D 7 ILE B 132 ASP B 134 -1 N ASP B 134 O PHE B 175 SHEET 1 E 2 LYS B 98 GLU B 103 0 SHEET 2 E 2 SER B 109 LYS B 113 -1 O VAL B 110 N CYS B 101 SHEET 1 F 4 GLY B 183 HIS B 187 0 SHEET 2 F 4 TRP B 272 ASN B 277 -1 O HIS B 273 N HIS B 187 SHEET 3 F 4 LYS B 204 PHE B 209 -1 N ARG B 205 O LEU B 276 SHEET 4 F 4 LEU B 255 GLN B 259 -1 O GLN B 259 N LYS B 204 LINK C HIS A 0 N MSE A 1 1555 1555 1.33 LINK C MSE A 1 N ASN A 2 1555 1555 1.33 LINK C LYS A 111 N MSE A 112 1555 1555 1.35 LINK C MSE A 112 N LYS A 113 1555 1555 1.35 LINK C LYS A 113 N MSE A 114 1555 1555 1.34 LINK C MSE A 114 N LYS A 115 1555 1555 1.34 LINK C TYR A 120 N MSE A 121 1555 1555 1.33 LINK C MSE A 121 N GLU A 122 1555 1555 1.33 LINK C VAL A 176 N MSE A 177 1555 1555 1.35 LINK C MSE A 177 N GLY A 178 1555 1555 1.34 LINK C HIS B 0 N MSE B 1 1555 1555 1.33 LINK C MSE B 1 N ASN B 2 1555 1555 1.33 LINK C LYS B 111 N MSE B 112 1555 1555 1.34 LINK C MSE B 112 N LYS B 113 1555 1555 1.34 LINK C LYS B 113 N MSE B 114 1555 1555 1.34 LINK C MSE B 114 N LYS B 115 1555 1555 1.34 LINK C TYR B 120 N MSE B 121 1555 1555 1.33 LINK C MSE B 121 N GLU B 122 1555 1555 1.33 LINK C VAL B 176 N MSE B 177 1555 1555 1.35 LINK C MSE B 177 N GLY B 178 1555 1555 1.35 LINK NE2 HIS A 187 NI NI A 336 1555 1555 2.33 LINK OD1 ASP A 189 NI NI A 336 1555 1555 2.35 LINK NE2 HIS A 273 NI NI A 336 1555 1555 2.33 LINK NE2 HIS B 187 NI NI B 336 1555 1555 2.34 LINK OD1 ASP B 189 NI NI B 336 1555 1555 2.42 LINK NE2 HIS B 273 NI NI B 336 1555 1555 2.33 LINK NI NI A 336 O HOH A 715 1555 1555 2.25 LINK NI NI A 336 O HOH A 717 1555 1555 2.39 LINK NI NI A 336 O HOH A 716 1555 1555 2.41 LINK NI NI B 336 O HOH B 356 1555 1555 2.28 LINK NI NI B 336 O HOH B 346 1555 1555 2.56 LINK NI NI B 336 O HOH B 354 1555 1555 2.32 LINK O PHE B 155 NA NA B 341 1555 1555 3.11 LINK NA NA B 341 O HOH B 398 1555 1555 3.16 SITE 1 AC1 6 HIS A 187 ASP A 189 HIS A 273 HOH A 715 SITE 2 AC1 6 HOH A 716 HOH A 717 SITE 1 AC2 2 LYS A 154 CL A 338 SITE 1 AC3 1 NA A 337 SITE 1 AC4 4 SER A 109 LYS A 111 SER A 136 HOH A 748 SITE 1 AC5 4 TYR A 131 THR A 184 ASN A 197 LYS A 204 SITE 1 AC6 6 GLU A 61 PRO A 66 HOH A 750 TYR B 67 SITE 2 AC6 6 GLY B 269 HOH B 369 SITE 1 AC7 6 HIS B 187 ASP B 189 HIS B 273 HOH B 346 SITE 2 AC7 6 HOH B 354 HOH B 356 SITE 1 AC8 1 LYS B 4 SITE 1 AC9 6 ALA B 75 GLU B 77 TRP B 79 HOH B 439 SITE 2 AC9 6 HOH B 547 HOH B 641 SITE 1 BC1 3 ASN B 197 THR B 285 ACT B 345 SITE 1 BC2 2 LEU B 87 GLU B 88 SITE 1 BC3 4 PHE B 155 PHE B 156 THR B 157 ASP B 158 SITE 1 BC4 1 VAL B 56 SITE 1 BC5 3 GLN B 97 LYS B 98 HOH B 665 SITE 1 BC6 5 SER B 109 LYS B 111 SER B 136 HOH B 406 SITE 2 BC6 5 HOH B 709 SITE 1 BC7 5 TYR B 131 THR B 184 ASN B 197 LYS B 204 SITE 2 BC7 5 CL B 339 CRYST1 49.440 102.030 98.218 90.00 95.89 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 0.020227 0.000000 0.002087 0.00000 SCALE2 0.000000 0.009801 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010235 0.00000