HEADER OXIDOREDUCTASE 31-MAY-10 3N9N TITLE CEKDM7A FROM C.ELEGANS, COMPLEX WITH H3K4ME3K9ME2 PEPTIDE AND NOG COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PHD DOMAIN, UNP RESIDUES 201-724; COMPND 5 SYNONYM: LYSINE DEMETHYLASE; COMPND 6 EC: 1.14.11.27; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: HISTONE H3 PEPTIDE; COMPND 10 CHAIN: B, C; COMPND 11 FRAGMENT: JMJC DOMAIN, UNP RESIDUES 2-33; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: H3K4ME3K9ME2 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_TAXID: 6239; SOURCE 4 GENE: F29B9.2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 13 ORGANISM_TAXID: 6239; SOURCE 14 OTHER_DETAILS: CHEMICAL SYNTHESIS, PURCHASED FROM A COMPANY KEYWDS HISTONE, METHYLATION, DEMETHYLASE, PHD, JMJC, FE(II) AND ALPHA-KG KEYWDS 2 (ALPHA-KETOGLUTARATE)-DEPENDENT DIOXYGENASE FAMILY, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.YANG,L.HU,P.WANG,H.HOU,C.D.CHEN,Y.XU REVDAT 3 01-NOV-23 3N9N 1 REMARK SEQADV LINK REVDAT 2 11-AUG-10 3N9N 1 JRNL REVDAT 1 30-JUN-10 3N9N 0 JRNL AUTH Y.YANG,L.HU,P.WANG,H.HOU,Y.LIN,Y.LIU,Z.LI,R.GONG,X.FENG, JRNL AUTH 2 L.ZHOU,W.ZHANG,Y.DONG,H.YANG,H.LIN,Y.WANG,C.D.CHEN,Y.XU JRNL TITL STRUCTURAL INSIGHTS INTO A DUAL-SPECIFICITY HISTONE JRNL TITL 2 DEMETHYLASE CEKDM7A FROM CAENORHABDITIS ELEGANS JRNL REF CELL RES. V. 20 886 2010 JRNL REFN ISSN 1001-0602 JRNL PMID 20567261 JRNL DOI 10.1038/CR.2010.86 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.070 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 26734 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1347 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 39.4814 - 4.9498 1.00 2769 137 0.1861 0.2374 REMARK 3 2 4.9498 - 3.9299 1.00 2651 132 0.1580 0.2018 REMARK 3 3 3.9299 - 3.4335 1.00 2564 164 0.1769 0.2133 REMARK 3 4 3.4335 - 3.1197 0.99 2591 141 0.2030 0.2636 REMARK 3 5 3.1197 - 2.8962 0.99 2567 135 0.2138 0.2871 REMARK 3 6 2.8962 - 2.7255 0.98 2514 131 0.2106 0.2708 REMARK 3 7 2.7255 - 2.5890 0.97 2498 122 0.2008 0.2625 REMARK 3 8 2.5890 - 2.4763 0.95 2418 153 0.2015 0.2782 REMARK 3 9 2.4763 - 2.3810 0.95 2424 114 0.1902 0.2520 REMARK 3 10 2.3810 - 2.2988 0.92 2391 118 0.1954 0.2316 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 : 0.34 REMARK 3 B_SOL : 56.94 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.19 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.97030 REMARK 3 B22 (A**2) : 0.09450 REMARK 3 B33 (A**2) : -7.06480 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 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 : 0.005 4242 REMARK 3 ANGLE : 0.915 5721 REMARK 3 CHIRALITY : 0.069 588 REMARK 3 PLANARITY : 0.006 740 REMARK 3 DIHEDRAL : 17.654 1583 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 3N9N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000059554. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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 : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27466 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.299 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.40 REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHASES REMARK 200 STARTING MODEL: PDB ENTRY 3N9M REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 3350, 0.2M SODIUM FLUORIDE, REMARK 280 0.1M BIS-TRIS OR HEPES, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 34.20000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.27500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.77150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.27500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.20000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.77150 REMARK 290 SMTRY3 4 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 GLU A 184 REMARK 465 PHE A 185 REMARK 465 HIS A 186 REMARK 465 MET A 187 REMARK 465 GLU A 188 REMARK 465 GLN A 189 REMARK 465 LYS A 190 REMARK 465 THR A 191 REMARK 465 ASP A 209 REMARK 465 LEU A 210 REMARK 465 ILE A 211 REMARK 465 ALA A 212 REMARK 465 LEU A 213 REMARK 465 GLU A 214 REMARK 465 GLU A 215 REMARK 465 GLU A 216 REMARK 465 LYS A 217 REMARK 465 LYS A 218 REMARK 465 LYS A 219 REMARK 465 GLU A 220 REMARK 465 LYS A 221 REMARK 465 GLU A 222 REMARK 465 LYS A 223 REMARK 465 PRO A 224 REMARK 465 LEU A 225 REMARK 465 MET A 226 REMARK 465 SER A 227 REMARK 465 LYS A 228 REMARK 465 LYS A 229 REMARK 465 LYS A 230 REMARK 465 SER A 231 REMARK 465 HIS A 232 REMARK 465 HIS A 233 REMARK 465 HIS A 234 REMARK 465 ASN A 705 REMARK 465 LYS A 706 REMARK 465 PRO A 707 REMARK 465 MET A 708 REMARK 465 GLY A 709 REMARK 465 LEU A 710 REMARK 465 LYS A 711 REMARK 465 ALA B 7 REMARK 465 ARG B 8 REMARK 465 MLY B 9 REMARK 465 SER B 10 REMARK 465 THR B 11 REMARK 465 GLY B 12 REMARK 465 GLY B 13 REMARK 465 LYS B 14 REMARK 465 ALA B 15 REMARK 465 PRO B 16 REMARK 465 ARG B 17 REMARK 465 LYS B 18 REMARK 465 GLN B 19 REMARK 465 LEU B 20 REMARK 465 ALA B 21 REMARK 465 THR B 22 REMARK 465 LYS B 23 REMARK 465 ALA B 24 REMARK 465 ALA B 25 REMARK 465 ARG B 26 REMARK 465 LYS B 27 REMARK 465 SER B 28 REMARK 465 ALA B 29 REMARK 465 PRO B 30 REMARK 465 ALA B 31 REMARK 465 SER B 32 REMARK 465 ALA C 1 REMARK 465 ARG C 2 REMARK 465 THR C 3 REMARK 465 M3L C 4 REMARK 465 ALA C 15 REMARK 465 PRO C 16 REMARK 465 ARG C 17 REMARK 465 LYS C 18 REMARK 465 GLN C 19 REMARK 465 LEU C 20 REMARK 465 ALA C 21 REMARK 465 THR C 22 REMARK 465 LYS C 23 REMARK 465 ALA C 24 REMARK 465 ALA C 25 REMARK 465 ARG C 26 REMARK 465 LYS C 27 REMARK 465 SER C 28 REMARK 465 ALA C 29 REMARK 465 PRO C 30 REMARK 465 ALA C 31 REMARK 465 SER C 32 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OH TYR A 292 O VAL A 306 2.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS A 193 108.90 -162.90 REMARK 500 CYS A 201 -47.37 78.37 REMARK 500 ASP A 238 -144.52 56.99 REMARK 500 PHE A 239 72.52 -119.62 REMARK 500 SER A 246 -62.61 -100.97 REMARK 500 PHE A 270 54.83 94.68 REMARK 500 THR A 278 -17.79 -147.82 REMARK 500 PRO A 371 151.02 -44.04 REMARK 500 TRP A 453 66.60 -117.37 REMARK 500 GLU A 468 42.54 -77.18 REMARK 500 VAL A 479 1.06 -150.68 REMARK 500 VAL A 627 -73.13 -115.92 REMARK 500 GLU A 638 -155.43 -109.83 REMARK 500 SER A 640 110.39 -169.53 REMARK 500 GLU A 646 37.83 -161.45 REMARK 500 GLU A 673 -138.98 -78.88 REMARK 500 LYS A 674 -173.36 -69.11 REMARK 500 ALA A 676 176.02 63.05 REMARK 500 THR C 6 30.39 -147.94 REMARK 500 THR C 11 -83.04 -117.78 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 FE2 A 1 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 OGA A 4 O2 REMARK 620 2 OGA A 4 O2' 79.4 REMARK 620 3 HOH A 7 O 91.2 92.0 REMARK 620 4 HIS A 495 NE2 172.4 95.0 83.9 REMARK 620 5 ASP A 497 OD2 90.5 169.0 92.4 95.5 REMARK 620 6 HIS A 567 NE2 94.7 91.6 173.6 90.6 85.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 2 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 198 SG REMARK 620 2 CYS A 201 SG 114.4 REMARK 620 3 HIS A 252 ND1 101.5 100.9 REMARK 620 4 CYS A 255 SG 106.4 103.4 130.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 3 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 244 SG REMARK 620 2 CYS A 247 SG 94.8 REMARK 620 3 CYS A 271 SG 117.7 112.4 REMARK 620 4 CYS A 274 SG 112.8 111.1 107.6 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 FE2 A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OGA A 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3N9L RELATED DB: PDB REMARK 900 LYSINE DEMETHYLASE WITH HISTONE H3(K4ME3) AND NOG REMARK 900 RELATED ID: 3N9M RELATED DB: PDB REMARK 900 APO LYSINE DEMETHYLASE REMARK 900 RELATED ID: 3N9O RELATED DB: PDB REMARK 900 LYSINE DEMETHYLASE WITH HISTONE H3(K4ME3) AND HISTONE H3(K9ME2) AND REMARK 900 NOG REMARK 900 RELATED ID: 3N9P RELATED DB: PDB REMARK 900 LYSINE DEMETHYLASE WITH HISTONE H3(K4ME3K27ME2) AND NOG REMARK 900 RELATED ID: 3N9Q RELATED DB: PDB REMARK 900 LYSINE DEMETHYLASE WITH HISTONE H3(K4ME3) AND HISTONE H3(K27ME2) REMARK 900 AND NOG DBREF 3N9N A 188 711 UNP Q9GYI0 Q9GYI0_CAEEL 201 724 DBREF 3N9N B 1 32 UNP P08898 H3_CAEEL 2 33 DBREF 3N9N C 1 32 UNP P08898 H3_CAEEL 2 33 SEQADV 3N9N GLU A 184 UNP Q9GYI0 EXPRESSION TAG SEQADV 3N9N PHE A 185 UNP Q9GYI0 EXPRESSION TAG SEQADV 3N9N HIS A 186 UNP Q9GYI0 EXPRESSION TAG SEQADV 3N9N MET A 187 UNP Q9GYI0 EXPRESSION TAG SEQRES 1 A 528 GLU PHE HIS MET GLU GLN LYS THR PRO LYS GLU SER ASP SEQRES 2 A 528 ARG CYS GLY GLY CYS GLY LYS PHE THR HIS GLU ASP ASP SEQRES 3 A 528 LEU ILE ALA LEU GLU GLU GLU LYS LYS LYS GLU LYS GLU SEQRES 4 A 528 LYS PRO LEU MET SER LYS LYS LYS SER HIS HIS HIS LYS SEQRES 5 A 528 LYS ASN ASP PHE GLN TRP ILE GLY CYS ASP SER CYS GLN SEQRES 6 A 528 THR TRP TYR HIS PHE LEU CYS SER GLY LEU GLU GLN PHE SEQRES 7 A 528 GLU TYR TYR LEU TYR GLU LYS PHE PHE CYS PRO LYS CYS SEQRES 8 A 528 VAL PRO HIS THR GLY HIS SER ILE ARG TYR LYS VAL VAL SEQRES 9 A 528 ALA PRO HIS ARG TYR ARG TRP TYR SER PRO ASN GLU LYS SEQRES 10 A 528 HIS LEU GLY ILE GLU VAL GLY SER LYS THR TRP ILE GLU SEQRES 11 A 528 ASP PHE ILE THR ARG GLU ASN THR VAL PRO SER PRO THR SEQRES 12 A 528 ASP ASP GLU VAL CYS ILE VAL GLU ASP GLY TYR GLU PHE SEQRES 13 A 528 ARG ARG GLU PHE GLU LYS LEU GLY GLY ALA ASP ASN TRP SEQRES 14 A 528 GLY LYS VAL PHE MET VAL LYS ASP MET ASP GLY LEU ASN SEQRES 15 A 528 MET THR MET PRO LYS PRO GLY PHE ASP LEU GLU ASP VAL SEQRES 16 A 528 VAL LYS ILE MET GLY SER ASP TYR GLU VAL ASP THR ILE SEQRES 17 A 528 ASP VAL TYR ASN GLN SER THR TYR SER MET LYS LEU ASP SEQRES 18 A 528 THR PHE ARG LYS LEU PHE ARG ASP THR LYS ASN ARG PRO SEQRES 19 A 528 LEU LEU TYR ASN PHE LEU SER LEU GLU PHE SER ASP ASN SEQRES 20 A 528 ASN GLU MET LYS GLU ILE ALA LYS PRO PRO ARG PHE VAL SEQRES 21 A 528 GLN GLU ILE SER MET VAL ASN ARG LEU TRP PRO ASP VAL SEQRES 22 A 528 SER GLY ALA GLU TYR ILE LYS LEU LEU GLN ARG GLU GLU SEQRES 23 A 528 TYR LEU PRO GLU ASP GLN ARG PRO LYS VAL GLU GLN PHE SEQRES 24 A 528 CYS LEU ALA GLY MET ALA GLY SER TYR THR ASP PHE HIS SEQRES 25 A 528 VAL ASP PHE GLY GLY SER SER VAL TYR TYR HIS ILE LEU SEQRES 26 A 528 LYS GLY GLU LYS ILE PHE TYR ILE ALA ALA PRO THR GLU SEQRES 27 A 528 GLN ASN PHE ALA ALA TYR GLN ALA HIS GLU THR SER PRO SEQRES 28 A 528 ASP THR THR THR TRP PHE GLY ASP ILE ALA ASN GLY ALA SEQRES 29 A 528 VAL LYS ARG VAL VAL ILE LYS GLU GLY GLN THR LEU LEU SEQRES 30 A 528 ILE PRO ALA GLY TRP ILE HIS ALA VAL LEU THR PRO VAL SEQRES 31 A 528 ASP SER LEU VAL PHE GLY GLY ASN PHE LEU HIS LEU GLY SEQRES 32 A 528 ASN LEU GLU MET GLN MET ARG VAL TYR HIS LEU GLU ASN SEQRES 33 A 528 ALA ILE ARG LYS GLU ILE ARG SER GLU GLU LYS PHE TYR SEQRES 34 A 528 PHE PRO ASN PHE GLU LEU LEU HIS TRP MET TYR MET ARG SEQRES 35 A 528 ASN VAL LEU LEU GLU LYS ILE THR GLU ALA ASN GLN GLU SEQRES 36 A 528 GLY SER ASP MET ARG GLU GLN GLU LYS ASN ILE TRP THR SEQRES 37 A 528 ALA SER GLN ILE MET LYS ALA GLU MET GLU ARG TRP MET SEQRES 38 A 528 ASP ARG GLU LEU ARG LEU GLY PRO GLU LYS ASN ALA ILE SEQRES 39 A 528 LEU PRO THR ASP ASP LYS ASN LYS ILE MET ILE SER VAL SEQRES 40 A 528 ARG LYS GLN ILE GLU ILE GLN THR LYS ILE GLN ASN ALA SEQRES 41 A 528 LYS ASN LYS PRO MET GLY LEU LYS SEQRES 1 B 32 ALA ARG THR M3L GLN THR ALA ARG MLY SER THR GLY GLY SEQRES 2 B 32 LYS ALA PRO ARG LYS GLN LEU ALA THR LYS ALA ALA ARG SEQRES 3 B 32 LYS SER ALA PRO ALA SER SEQRES 1 C 32 ALA ARG THR M3L GLN THR ALA ARG MLY SER THR GLY GLY SEQRES 2 C 32 LYS ALA PRO ARG LYS GLN LEU ALA THR LYS ALA ALA ARG SEQRES 3 C 32 LYS SER ALA PRO ALA SER MODRES 3N9N M3L B 4 LYS N-TRIMETHYLLYSINE MODRES 3N9N MLY C 9 LYS N-DIMETHYL-LYSINE HET M3L B 4 12 HET MLY C 9 11 HET FE2 A 1 1 HET ZN A 2 1 HET ZN A 3 1 HET OGA A 4 10 HETNAM M3L N-TRIMETHYLLYSINE HETNAM MLY N-DIMETHYL-LYSINE HETNAM FE2 FE (II) ION HETNAM ZN ZINC ION HETNAM OGA N-OXALYLGLYCINE FORMUL 2 M3L C9 H21 N2 O2 1+ FORMUL 3 MLY C8 H18 N2 O2 FORMUL 4 FE2 FE 2+ FORMUL 5 ZN 2(ZN 2+) FORMUL 7 OGA C4 H5 N O5 FORMUL 8 HOH *290(H2 O) HELIX 1 1 LYS A 193 ARG A 197 5 5 HELIX 2 2 LEU A 254 SER A 256 5 3 HELIX 3 3 GLU A 259 TYR A 263 5 5 HELIX 4 4 CYS A 274 THR A 278 5 5 HELIX 5 5 SER A 296 LYS A 300 5 5 HELIX 6 6 SER A 308 GLU A 319 1 12 HELIX 7 7 ASN A 320 VAL A 322 5 3 HELIX 8 8 GLY A 336 LEU A 346 1 11 HELIX 9 9 GLY A 347 TRP A 352 5 6 HELIX 10 10 ASP A 374 GLY A 383 1 10 HELIX 11 11 LEU A 403 ASP A 412 1 10 HELIX 12 12 GLU A 432 ILE A 436 5 5 HELIX 13 13 PRO A 440 SER A 447 1 8 HELIX 14 14 SER A 447 TRP A 453 1 7 HELIX 15 15 SER A 457 ARG A 467 1 11 HELIX 16 16 PRO A 472 ARG A 476 5 5 HELIX 17 17 ASP A 497 SER A 501 5 5 HELIX 18 18 THR A 520 SER A 533 1 14 HELIX 19 19 TRP A 539 ALA A 544 5 6 HELIX 20 20 HIS A 584 GLY A 586 5 3 HELIX 21 21 ASN A 587 ILE A 605 1 19 HELIX 22 22 GLU A 608 TYR A 612 5 5 HELIX 23 23 ASN A 615 VAL A 627 1 13 HELIX 24 24 VAL A 627 GLU A 638 1 12 HELIX 25 25 GLU A 646 GLY A 671 1 26 HELIX 26 26 PRO A 679 LYS A 704 1 26 SHEET 1 A 3 TRP A 250 HIS A 252 0 SHEET 2 A 3 GLN A 240 GLY A 243 -1 N ILE A 242 O TYR A 251 SHEET 3 A 3 THR B 3 GLN B 5 -1 O M3L B 4 N TRP A 241 SHEET 1 B 2 TYR A 266 LYS A 268 0 SHEET 2 B 2 ILE A 282 ARG A 283 -1 O ILE A 282 N LYS A 268 SHEET 1 C 6 VAL A 330 ASP A 335 0 SHEET 2 C 6 VAL A 355 ASP A 360 1 O MET A 357 N VAL A 333 SHEET 3 C 6 THR A 558 ILE A 561 -1 O THR A 558 N VAL A 358 SHEET 4 C 6 SER A 502 ALA A 517 -1 N VAL A 503 O ILE A 561 SHEET 5 C 6 ILE A 566 PHE A 582 -1 O PHE A 578 N HIS A 506 SHEET 6 C 6 SER A 490 HIS A 495 -1 N SER A 490 O THR A 571 SHEET 1 D 7 SER A 397 LYS A 402 0 SHEET 2 D 7 GLU A 387 ASP A 392 -1 N ASP A 392 O SER A 397 SHEET 3 D 7 TYR A 420 GLU A 426 -1 O ASN A 421 N ILE A 391 SHEET 4 D 7 PHE A 482 GLY A 486 -1 O CYS A 483 N LEU A 425 SHEET 5 D 7 ILE A 566 PHE A 582 -1 O VAL A 577 N LEU A 484 SHEET 6 D 7 SER A 502 ALA A 517 -1 N HIS A 506 O PHE A 578 SHEET 7 D 7 LYS A 549 LYS A 554 -1 O ILE A 553 N LYS A 512 LINK C THR B 3 N M3L B 4 1555 1555 1.33 LINK C M3L B 4 N GLN B 5 1555 1555 1.33 LINK C ARG C 8 N MLY C 9 1555 1555 1.33 LINK C MLY C 9 N SER C 10 1555 1555 1.33 LINK FE FE2 A 1 O2 OGA A 4 1555 1555 2.23 LINK FE FE2 A 1 O2' OGA A 4 1555 1555 2.27 LINK FE FE2 A 1 O HOH A 7 1555 1555 2.16 LINK FE FE2 A 1 NE2 HIS A 495 1555 1555 2.25 LINK FE FE2 A 1 OD2 ASP A 497 1555 1555 2.23 LINK FE FE2 A 1 NE2 HIS A 567 1555 1555 2.31 LINK ZN ZN A 2 SG CYS A 198 1555 1555 2.50 LINK ZN ZN A 2 SG CYS A 201 1555 1555 2.54 LINK ZN ZN A 2 ND1 HIS A 252 1555 1555 2.18 LINK ZN ZN A 2 SG CYS A 255 1555 1555 2.49 LINK ZN ZN A 3 SG CYS A 244 1555 1555 2.44 LINK ZN ZN A 3 SG CYS A 247 1555 1555 2.58 LINK ZN ZN A 3 SG CYS A 271 1555 1555 2.58 LINK ZN ZN A 3 SG CYS A 274 1555 1555 2.63 CISPEP 1 CYS A 198 GLY A 199 0 3.10 CISPEP 2 GLY A 199 GLY A 200 0 8.88 CISPEP 3 GLY A 200 CYS A 201 0 3.07 CISPEP 4 PHE A 269 PHE A 270 0 5.99 CISPEP 5 VAL A 306 GLY A 307 0 -14.85 CISPEP 6 GLY A 639 SER A 640 0 -4.29 CISPEP 7 ALA A 676 ILE A 677 0 -1.67 CISPEP 8 GLY C 13 LYS C 14 0 0.74 SITE 1 AC1 5 OGA A 4 HOH A 7 HIS A 495 ASP A 497 SITE 2 AC1 5 HIS A 567 SITE 1 AC2 4 CYS A 198 CYS A 201 HIS A 252 CYS A 255 SITE 1 AC3 4 CYS A 244 CYS A 247 CYS A 271 CYS A 274 SITE 1 AC4 11 FE2 A 1 HOH A 33 ASN A 421 THR A 492 SITE 2 AC4 11 HIS A 495 ASP A 497 TYR A 505 LYS A 512 SITE 3 AC4 11 HIS A 567 VAL A 569 MLY C 9 CRYST1 68.400 85.543 102.550 90.00 90.00 90.00 P 21 21 21 8 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 0.014620 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011690 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009751 0.00000