HEADER OXIDOREDUCTASE 14-MAY-07 2PXJ TITLE THE COMPLEX STRUCTURE OF JMJD2A AND MONOMETHYLATED H3K36 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC CORE; COMPND 5 SYNONYM: JUMONJI DOMAIN-CONTAINING PROTEIN 2A; COMPND 6 EC: 1.14.11.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: MONOMETHYLATED HISTONE H3K36 PEPTIDE; COMPND 10 CHAIN: I, J; 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: JMJD2A, JHDM3A, JMJD2, KIAA0677; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX4T2; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN HUMANS KEYWDS JMJD2A; HISTONE DEMETHYLASE; JMJC; H3K36, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.CHEN,J.ZANG,J.KAPPLER,X.HONG,F.CRAWFORD,G.ZHANG REVDAT 4 30-AUG-23 2PXJ 1 REMARK LINK REVDAT 3 24-FEB-09 2PXJ 1 VERSN REVDAT 2 26-JUN-07 2PXJ 1 ATOM HETATM JRNL REVDAT 1 12-JUN-07 2PXJ 0 JRNL AUTH Z.CHEN,J.ZANG,J.KAPPLER,X.HONG,F.CRAWFORD,Q.WANG,F.LAN, JRNL AUTH 2 C.JIANG,J.WHETSTINE,S.DAI,K.HANSEN,Y.SHI,G.ZHANG JRNL TITL STRUCTURAL BASIS OF THE RECOGNITION OF A METHYLATED HISTONE JRNL TITL 2 TAIL BY JMJD2A JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 10818 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 17567753 JRNL DOI 10.1073/PNAS.0704525104 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 95055.510 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.7 REMARK 3 NUMBER OF REFLECTIONS : 54154 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) : 0.256 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2196 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 67.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6325 REMARK 3 BIN R VALUE (WORKING SET) : 0.4220 REMARK 3 BIN FREE R VALUE : 0.4140 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 275 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.025 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5700 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 151 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.47000 REMARK 3 B22 (A**2) : 4.00000 REMARK 3 B33 (A**2) : -0.53000 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) : 0.41 REMARK 3 ESD FROM SIGMAA (A) : 0.48 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.46 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.54 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.940 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 30.61 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 : WATER.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NOG.PAR REMARK 3 PARAMETER FILE 5 : M1L.PAR REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NOG.TOP REMARK 3 TOPOLOGY FILE 5 : M1L.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2PXJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAY-07. REMARK 100 THE DEPOSITION ID IS D_1000042890. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID 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 : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58067 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.200 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.53500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 2GP3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15-17% PEG 5000 MME, PH 8.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 50.43150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 75.08600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 50.43150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 75.08600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, I 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, J 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 ALA B 2 REMARK 465 SER B 3 REMARK 465 GLU B 4 REMARK 465 SER B 5 REMARK 465 GLU B 6 REMARK 465 THR B 7 REMARK 465 LEU B 8 REMARK 465 ASN B 9 REMARK 465 THR B 347 REMARK 465 PRO B 348 REMARK 465 ARG I 0 REMARK 465 LYS I 1 REMARK 465 SER I 2 REMARK 465 ALA I 3 REMARK 465 PRO I 4 REMARK 465 ALA I 5 REMARK 465 THR I 6 REMARK 465 PRO I 12 REMARK 465 HIS I 13 REMARK 465 ARG I 14 REMARK 465 TYR I 15 REMARK 465 ARG I 16 REMARK 465 PRO I 17 REMARK 465 GLY I 18 REMARK 465 THR I 19 REMARK 465 VAL I 20 REMARK 465 LEU I 21 REMARK 465 ARG J 0 REMARK 465 LYS J 1 REMARK 465 SER J 2 REMARK 465 ALA J 3 REMARK 465 PRO J 4 REMARK 465 ALA J 5 REMARK 465 PRO J 12 REMARK 465 HIS J 13 REMARK 465 ARG J 14 REMARK 465 TYR J 15 REMARK 465 ARG J 16 REMARK 465 PRO J 17 REMARK 465 GLY J 18 REMARK 465 THR J 19 REMARK 465 VAL J 20 REMARK 465 LEU J 21 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 SER A 3 58.91 -108.20 REMARK 500 GLU A 4 -21.77 72.34 REMARK 500 LEU A 65 137.52 -37.61 REMARK 500 SER A 112 -74.43 -99.26 REMARK 500 PRO A 129 107.63 -38.78 REMARK 500 ARG A 152 72.93 -156.36 REMARK 500 VAL A 171 -60.54 -91.63 REMARK 500 MET A 192 19.96 59.51 REMARK 500 CYS A 234 103.30 -169.97 REMARK 500 ALA A 236 42.65 -86.59 REMARK 500 LYS A 310 71.27 -115.00 REMARK 500 ASP A 311 6.12 -173.15 REMARK 500 ASN A 338 44.29 -96.57 REMARK 500 LEU B 65 136.42 -35.14 REMARK 500 SER B 103 155.53 -48.10 REMARK 500 SER B 112 -73.73 -99.88 REMARK 500 ARG B 152 74.82 -155.08 REMARK 500 LYS B 182 -0.46 67.38 REMARK 500 CYS B 234 108.29 -170.45 REMARK 500 ALA B 236 43.63 -87.49 REMARK 500 LYS B 310 75.27 -116.19 REMARK 500 ASP B 311 3.91 -176.55 REMARK 500 ASN B 338 44.19 -100.62 REMARK 500 HIS B 343 4.07 -60.59 REMARK 500 LEU B 345 -72.21 -24.72 REMARK 500 MLZ I 10 -156.62 -72.67 REMARK 500 MLZ J 10 -156.42 -72.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 MLZ J 10 10.03 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 A3001 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 188 NE2 REMARK 620 2 GLU A 190 OE1 106.1 REMARK 620 3 HIS A 276 NE2 98.3 89.2 REMARK 620 4 OGA A5001 O2' 96.6 151.0 105.4 REMARK 620 5 OGA A5001 O2 156.1 84.4 103.4 68.1 REMARK 620 6 HOH A5077 O 85.5 87.1 175.4 76.8 73.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 234 SG REMARK 620 2 HIS A 240 NE2 102.3 REMARK 620 3 CYS A 306 SG 121.0 118.5 REMARK 620 4 CYS A 308 SG 110.7 85.7 112.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 B4001 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 188 NE2 REMARK 620 2 GLU B 190 OE1 111.8 REMARK 620 3 HIS B 276 NE2 103.4 87.7 REMARK 620 4 OGA B6001 O2' 97.8 149.4 92.9 REMARK 620 5 OGA B6001 O2 168.3 79.8 77.8 70.5 REMARK 620 6 HOH B6043 O 89.9 87.9 166.7 84.5 89.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B2001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 234 SG REMARK 620 2 HIS B 240 NE2 108.9 REMARK 620 3 CYS B 306 SG 123.9 112.6 REMARK 620 4 CYS B 308 SG 108.1 82.4 113.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 A 3001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 B 4001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OGA A 5001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OGA B 6001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2P5B RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH TRIMETHYLATED H3K36 PEPTIDE REMARK 900 RELATED ID: 2GP3 RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITHOUT PEPTIDE REMARK 900 RELATED ID: 2GP5 RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITHOUT PEPTIDE DBREF 2PXJ A 2 348 UNP O75164 JHD3A_HUMAN 2 348 DBREF 2PXJ B 2 348 UNP O75164 JHD3A_HUMAN 2 348 DBREF 2PXJ I 0 21 PDB 2PXJ 2PXJ 0 21 DBREF 2PXJ J 0 21 PDB 2PXJ 2PXJ 0 21 SEQRES 1 A 347 ALA SER GLU SER GLU THR LEU ASN PRO SER ALA ARG ILE SEQRES 2 A 347 MET THR PHE TYR PRO THR MET GLU GLU PHE ARG ASN PHE SEQRES 3 A 347 SER ARG TYR ILE ALA TYR ILE GLU SER GLN GLY ALA HIS SEQRES 4 A 347 ARG ALA GLY LEU ALA LYS VAL VAL PRO PRO LYS GLU TRP SEQRES 5 A 347 LYS PRO ARG ALA SER TYR ASP ASP ILE ASP ASP LEU VAL SEQRES 6 A 347 ILE PRO ALA PRO ILE GLN GLN LEU VAL THR GLY GLN SER SEQRES 7 A 347 GLY LEU PHE THR GLN TYR ASN ILE GLN LYS LYS ALA MET SEQRES 8 A 347 THR VAL ARG GLU PHE ARG LYS ILE ALA ASN SER ASP LYS SEQRES 9 A 347 TYR CYS THR PRO ARG TYR SER GLU PHE GLU GLU LEU GLU SEQRES 10 A 347 ARG LYS TYR TRP LYS ASN LEU THR PHE ASN PRO PRO ILE SEQRES 11 A 347 TYR GLY ALA ASP VAL ASN GLY THR LEU TYR GLU LYS HIS SEQRES 12 A 347 VAL ASP GLU TRP ASN ILE GLY ARG LEU ARG THR ILE LEU SEQRES 13 A 347 ASP LEU VAL GLU LYS GLU SER GLY ILE THR ILE GLU GLY SEQRES 14 A 347 VAL ASN THR PRO TYR LEU TYR PHE GLY MET TRP LYS THR SEQRES 15 A 347 SER PHE ALA TRP HIS THR GLU ASP MET ASP LEU TYR SER SEQRES 16 A 347 ILE ASN TYR LEU HIS PHE GLY GLU PRO LYS SER TRP TYR SEQRES 17 A 347 SER VAL PRO PRO GLU HIS GLY LYS ARG LEU GLU ARG LEU SEQRES 18 A 347 ALA LYS GLY PHE PHE PRO GLY SER ALA GLN SER CYS GLU SEQRES 19 A 347 ALA PHE LEU ARG HIS LYS MET THR LEU ILE SER PRO LEU SEQRES 20 A 347 MET LEU LYS LYS TYR GLY ILE PRO PHE ASP LYS VAL THR SEQRES 21 A 347 GLN GLU ALA GLY GLU PHE MET ILE THR PHE PRO TYR GLY SEQRES 22 A 347 TYR HIS ALA GLY PHE ASN HIS GLY PHE ASN CYS ALA GLU SEQRES 23 A 347 SER THR ASN PHE ALA THR ARG ARG TRP ILE GLU TYR GLY SEQRES 24 A 347 LYS GLN ALA VAL LEU CYS SER CYS ARG LYS ASP MET VAL SEQRES 25 A 347 LYS ILE SER MET ASP VAL PHE VAL ARG LYS PHE GLN PRO SEQRES 26 A 347 GLU ARG TYR LYS LEU TRP LYS ALA GLY LYS ASP ASN THR SEQRES 27 A 347 VAL ILE ASP HIS THR LEU PRO THR PRO SEQRES 1 B 347 ALA SER GLU SER GLU THR LEU ASN PRO SER ALA ARG ILE SEQRES 2 B 347 MET THR PHE TYR PRO THR MET GLU GLU PHE ARG ASN PHE SEQRES 3 B 347 SER ARG TYR ILE ALA TYR ILE GLU SER GLN GLY ALA HIS SEQRES 4 B 347 ARG ALA GLY LEU ALA LYS VAL VAL PRO PRO LYS GLU TRP SEQRES 5 B 347 LYS PRO ARG ALA SER TYR ASP ASP ILE ASP ASP LEU VAL SEQRES 6 B 347 ILE PRO ALA PRO ILE GLN GLN LEU VAL THR GLY GLN SER SEQRES 7 B 347 GLY LEU PHE THR GLN TYR ASN ILE GLN LYS LYS ALA MET SEQRES 8 B 347 THR VAL ARG GLU PHE ARG LYS ILE ALA ASN SER ASP LYS SEQRES 9 B 347 TYR CYS THR PRO ARG TYR SER GLU PHE GLU GLU LEU GLU SEQRES 10 B 347 ARG LYS TYR TRP LYS ASN LEU THR PHE ASN PRO PRO ILE SEQRES 11 B 347 TYR GLY ALA ASP VAL ASN GLY THR LEU TYR GLU LYS HIS SEQRES 12 B 347 VAL ASP GLU TRP ASN ILE GLY ARG LEU ARG THR ILE LEU SEQRES 13 B 347 ASP LEU VAL GLU LYS GLU SER GLY ILE THR ILE GLU GLY SEQRES 14 B 347 VAL ASN THR PRO TYR LEU TYR PHE GLY MET TRP LYS THR SEQRES 15 B 347 SER PHE ALA TRP HIS THR GLU ASP MET ASP LEU TYR SER SEQRES 16 B 347 ILE ASN TYR LEU HIS PHE GLY GLU PRO LYS SER TRP TYR SEQRES 17 B 347 SER VAL PRO PRO GLU HIS GLY LYS ARG LEU GLU ARG LEU SEQRES 18 B 347 ALA LYS GLY PHE PHE PRO GLY SER ALA GLN SER CYS GLU SEQRES 19 B 347 ALA PHE LEU ARG HIS LYS MET THR LEU ILE SER PRO LEU SEQRES 20 B 347 MET LEU LYS LYS TYR GLY ILE PRO PHE ASP LYS VAL THR SEQRES 21 B 347 GLN GLU ALA GLY GLU PHE MET ILE THR PHE PRO TYR GLY SEQRES 22 B 347 TYR HIS ALA GLY PHE ASN HIS GLY PHE ASN CYS ALA GLU SEQRES 23 B 347 SER THR ASN PHE ALA THR ARG ARG TRP ILE GLU TYR GLY SEQRES 24 B 347 LYS GLN ALA VAL LEU CYS SER CYS ARG LYS ASP MET VAL SEQRES 25 B 347 LYS ILE SER MET ASP VAL PHE VAL ARG LYS PHE GLN PRO SEQRES 26 B 347 GLU ARG TYR LYS LEU TRP LYS ALA GLY LYS ASP ASN THR SEQRES 27 B 347 VAL ILE ASP HIS THR LEU PRO THR PRO SEQRES 1 I 22 ARG LYS SER ALA PRO ALA THR GLY GLY VAL MLZ LYS PRO SEQRES 2 I 22 HIS ARG TYR ARG PRO GLY THR VAL LEU SEQRES 1 J 22 ARG LYS SER ALA PRO ALA THR GLY GLY VAL MLZ LYS PRO SEQRES 2 J 22 HIS ARG TYR ARG PRO GLY THR VAL LEU MODRES 2PXJ MLZ I 10 LYS N-METHYL-LYSINE MODRES 2PXJ MLZ J 10 LYS N-METHYL-LYSINE HET MLZ I 10 10 HET MLZ J 10 10 HET ZN A1001 1 HET FE2 A3001 1 HET OGA A5001 10 HET ZN B2001 1 HET FE2 B4001 1 HET OGA B6001 10 HETNAM MLZ N-METHYL-LYSINE HETNAM ZN ZINC ION HETNAM FE2 FE (II) ION HETNAM OGA N-OXALYLGLYCINE FORMUL 3 MLZ 2(C7 H16 N2 O2) FORMUL 5 ZN 2(ZN 2+) FORMUL 6 FE2 2(FE 2+) FORMUL 7 OGA 2(C4 H5 N O5) FORMUL 11 HOH *151(H2 O) HELIX 1 1 THR A 20 ARG A 25 1 6 HELIX 2 2 ASN A 26 GLN A 37 1 12 HELIX 3 3 GLY A 38 ALA A 42 5 5 HELIX 4 4 VAL A 94 SER A 103 1 10 HELIX 5 5 GLU A 113 LEU A 125 1 13 HELIX 6 6 THR A 155 LEU A 157 5 3 HELIX 7 7 ASP A 158 GLY A 165 1 8 HELIX 8 8 GLU A 190 LEU A 194 5 5 HELIX 9 9 PRO A 212 GLU A 214 5 3 HELIX 10 10 HIS A 215 PHE A 227 1 13 HELIX 11 11 PHE A 227 CYS A 234 1 8 HELIX 12 12 ALA A 236 LYS A 241 5 6 HELIX 13 13 SER A 246 TYR A 253 1 8 HELIX 14 14 ARG A 295 ALA A 303 1 9 HELIX 15 15 MET A 317 GLN A 325 1 9 HELIX 16 16 GLN A 325 ALA A 334 1 10 HELIX 17 17 THR B 20 ARG B 25 1 6 HELIX 18 18 ASN B 26 GLN B 37 1 12 HELIX 19 19 GLY B 38 ALA B 42 5 5 HELIX 20 20 VAL B 94 SER B 103 1 10 HELIX 21 21 GLU B 113 LEU B 125 1 13 HELIX 22 22 THR B 155 LEU B 157 5 3 HELIX 23 23 ASP B 158 GLY B 165 1 8 HELIX 24 24 GLU B 190 LEU B 194 5 5 HELIX 25 25 PRO B 212 GLU B 214 5 3 HELIX 26 26 HIS B 215 PHE B 227 1 13 HELIX 27 27 PHE B 227 CYS B 234 1 8 HELIX 28 28 ALA B 236 LYS B 241 5 6 HELIX 29 29 SER B 246 TYR B 253 1 8 HELIX 30 30 ARG B 295 ALA B 303 1 9 HELIX 31 31 MET B 317 GLN B 325 1 9 HELIX 32 32 GLN B 325 ALA B 334 1 10 SHEET 1 A10 MET A 15 PHE A 17 0 SHEET 2 A10 LEU A 44 VAL A 47 1 O LYS A 46 N MET A 15 SHEET 3 A10 PHE A 267 THR A 270 -1 O ILE A 269 N ALA A 45 SHEET 4 A10 TYR A 195 GLY A 203 -1 N ASN A 198 O MET A 268 SHEET 5 A10 ASN A 284 PHE A 291 -1 O GLU A 287 N TYR A 199 SHEET 6 A10 TYR A 175 GLY A 179 -1 N TYR A 177 O ALA A 286 SHEET 7 A10 ILE A 131 ASN A 137 -1 N VAL A 136 O LEU A 176 SHEET 8 A10 ILE A 71 GLN A 78 -1 N ILE A 71 O TYR A 132 SHEET 9 A10 LEU A 81 GLN A 88 -1 O ILE A 87 N GLN A 72 SHEET 10 A10 THR A 243 ILE A 245 -1 O LEU A 244 N PHE A 82 SHEET 1 B 2 VAL A 66 ILE A 67 0 SHEET 2 B 2 MET A 92 THR A 93 -1 O MET A 92 N ILE A 67 SHEET 1 C 4 SER A 184 HIS A 188 0 SHEET 2 C 4 TYR A 275 ASN A 280 -1 O GLY A 278 N PHE A 185 SHEET 3 C 4 LYS A 206 VAL A 211 -1 N VAL A 211 O TYR A 275 SHEET 4 C 4 ASP A 258 GLN A 262 -1 O VAL A 260 N TRP A 208 SHEET 1 D10 MET B 15 PHE B 17 0 SHEET 2 D10 LEU B 44 VAL B 47 1 O LYS B 46 N MET B 15 SHEET 3 D10 PHE B 267 THR B 270 -1 O PHE B 267 N VAL B 47 SHEET 4 D10 TYR B 195 GLY B 203 -1 N ASN B 198 O MET B 268 SHEET 5 D10 ASN B 284 PHE B 291 -1 O GLU B 287 N TYR B 199 SHEET 6 D10 TYR B 175 GLY B 179 -1 N TYR B 177 O ALA B 286 SHEET 7 D10 ILE B 131 ASN B 137 -1 N VAL B 136 O LEU B 176 SHEET 8 D10 ILE B 71 GLN B 78 -1 N ILE B 71 O TYR B 132 SHEET 9 D10 LEU B 81 GLN B 88 -1 O ILE B 87 N GLN B 72 SHEET 10 D10 THR B 243 ILE B 245 -1 O LEU B 244 N PHE B 82 SHEET 1 E 2 VAL B 66 ILE B 67 0 SHEET 2 E 2 MET B 92 THR B 93 -1 O MET B 92 N ILE B 67 SHEET 1 F 4 SER B 184 HIS B 188 0 SHEET 2 F 4 TYR B 275 ASN B 280 -1 O GLY B 278 N PHE B 185 SHEET 3 F 4 LYS B 206 VAL B 211 -1 N TYR B 209 O ALA B 277 SHEET 4 F 4 ASP B 258 GLN B 262 -1 O VAL B 260 N TRP B 208 LINK C VAL I 9 N MLZ I 10 1555 1555 1.36 LINK C MLZ I 10 N LYS I 11 1555 1555 1.37 LINK C VAL J 9 N MLZ J 10 1555 1555 1.36 LINK C MLZ J 10 N LYS J 11 1555 1555 1.37 LINK NE2 HIS A 188 FE FE2 A3001 1555 1555 2.45 LINK OE1 GLU A 190 FE FE2 A3001 1555 1555 2.10 LINK SG CYS A 234 ZN ZN A1001 1555 1555 2.44 LINK NE2 HIS A 240 ZN ZN A1001 1555 1555 2.19 LINK NE2 HIS A 276 FE FE2 A3001 1555 1555 2.17 LINK SG CYS A 306 ZN ZN A1001 1555 1555 2.26 LINK SG CYS A 308 ZN ZN A1001 1555 1555 2.51 LINK FE FE2 A3001 O2' OGA A5001 1555 1555 2.38 LINK FE FE2 A3001 O2 OGA A5001 1555 1555 2.63 LINK FE FE2 A3001 O HOH A5077 1555 1555 2.66 LINK NE2 HIS B 188 FE FE2 B4001 1555 1555 2.25 LINK OE1 GLU B 190 FE FE2 B4001 1555 1555 2.17 LINK SG CYS B 234 ZN ZN B2001 1555 1555 2.37 LINK NE2 HIS B 240 ZN ZN B2001 1555 1555 2.25 LINK NE2 HIS B 276 FE FE2 B4001 1555 1555 2.18 LINK SG CYS B 306 ZN ZN B2001 1555 1555 2.39 LINK SG CYS B 308 ZN ZN B2001 1555 1555 2.45 LINK FE FE2 B4001 O2' OGA B6001 1555 1555 2.48 LINK FE FE2 B4001 O2 OGA B6001 1555 1555 2.36 LINK FE FE2 B4001 O HOH B6043 1555 1555 2.67 SITE 1 AC1 4 CYS A 234 HIS A 240 CYS A 306 CYS A 308 SITE 1 AC2 4 CYS B 234 HIS B 240 CYS B 306 CYS B 308 SITE 1 AC3 5 HIS A 188 GLU A 190 HIS A 276 OGA A5001 SITE 2 AC3 5 HOH A5077 SITE 1 AC4 5 HIS B 188 GLU B 190 HIS B 276 OGA B6001 SITE 2 AC4 5 HOH B6043 SITE 1 AC5 11 TYR A 132 TYR A 177 PHE A 185 HIS A 188 SITE 2 AC5 11 GLU A 190 SER A 196 ASN A 198 LYS A 206 SITE 3 AC5 11 HIS A 276 SER A 288 FE2 A3001 SITE 1 AC6 11 TYR B 132 PHE B 185 HIS B 188 GLU B 190 SITE 2 AC6 11 SER B 196 ASN B 198 LYS B 206 TRP B 208 SITE 3 AC6 11 THR B 270 HIS B 276 FE2 B4001 CRYST1 100.863 150.172 57.317 90.00 90.00 90.00 P 21 21 2 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 0.009914 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006659 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017447 0.00000