PDB Short entry for 5JHN HEADER TRANSFERASE 21-APR-16 5JHN TITLE STRUCTURE OF G9A SET-DOMAIN WITH HISTONE H3K9ALA MUTANT PEPTIDE AND TITLE 2 BOUND S-ADENOSYLMETHIONINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE EHMT2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 882-1155; COMPND 5 SYNONYM: EUCHROMATIC HISTONE-LYSINE N-METHYLTRANSFERASE 2,HLA-B- COMPND 6 ASSOCIATED TRANSCRIPT 8,HISTONE H3-K9 METHYLTRANSFERASE 3,H3-K9- COMPND 7 HMTASE 3,LYSINE N-METHYLTRANSFERASE 1C,PROTEIN G9A; COMPND 8 EC: 2.1.1.-,2.1.1.43; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: HISTONE H3.1 PEPTIDE WITH K9A MUTATION; COMPND 12 CHAIN: F, G; COMPND 13 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: EHMT2, BAT8, C6ORF30, G9A, KMT1C, NG36; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) ROSETTA; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS SET-DOMAIN, HISTONE METHYL TRANSFERASE, HISTONE PEPTIDE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.JAYARAM,S.F.BELLON,F.POY REVDAT 2 06-MAR-24 5JHN 1 JRNL REMARK LINK REVDAT 1 06-JUL-16 5JHN 0 JRNL AUTH H.JAYARAM,D.HOELPER,S.U.JAIN,N.CANTONE,S.M.LUNDGREN,F.POY, JRNL AUTH 2 C.D.ALLIS,R.CUMMINGS,S.BELLON,P.W.LEWIS JRNL TITL S-ADENOSYL METHIONINE IS NECESSARY FOR INHIBITION OF THE JRNL TITL 2 METHYLTRANSFERASE G9A BY THE LYSINE 9 TO METHIONINE MUTATION JRNL TITL 3 ON HISTONE H3. JRNL REF PROC.NATL.ACAD.SCI.USA V. 113 6182 2016 JRNL REFN ESSN 1091-6490 JRNL PMID 27185940 JRNL DOI 10.1073/PNAS.1605523113 REMARK 2 REMARK 2 RESOLUTION. 1.67 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 70175 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 + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3723 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.67 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.71 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4869 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.3120 REMARK 3 BIN FREE R VALUE SET COUNT : 253 REMARK 3 BIN FREE R VALUE : 0.3510 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4482 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 62 REMARK 3 SOLVENT ATOMS : 154 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.88000 REMARK 3 B22 (A**2) : 1.09000 REMARK 3 B33 (A**2) : 0.77000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.51000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.108 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.105 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.092 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.882 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4688 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4294 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6330 ; 1.884 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9856 ; 1.235 ; 3.005 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 560 ; 6.223 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 242 ;29.799 ;23.719 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 799 ;14.895 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 43 ;14.249 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 674 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5320 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1133 ; 0.005 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2246 ; 3.060 ; 3.366 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2245 ; 3.049 ; 3.366 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2801 ; 4.117 ; 5.030 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2802 ; 4.117 ; 5.031 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2442 ; 3.974 ; 3.784 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2443 ; 3.974 ; 3.785 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3529 ; 5.910 ; 5.503 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5288 ; 7.368 ;26.988 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5289 ; 7.367 ;26.992 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 919 1188 B 919 1188 15967 0.09 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5JHN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000220603. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-12 REMARK 200 TEMPERATURE (KELVIN) : 175 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.010 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70175 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.670 REMARK 200 RESOLUTION RANGE LOW (A) : 34.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.6700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL 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: MAD REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M TRI-AMMONIUM CITRATE PH 7 AND REMARK 280 20% W/V POLYETHYLENE GLYCOL 3350, VAPOR DIFFUSION, TEMPERATURE REMARK 280 298K 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 39.13500 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, F, B, G 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 LEU A 1189 REMARK 465 THR F 3 REMARK 465 GLY F 12 REMARK 465 GLY F 13 REMARK 465 ILE B 916 REMARK 465 ARG B 917 REMARK 465 THR B 918 REMARK 465 ASN B 1091 REMARK 465 LYS B 1092 REMARK 465 ASP B 1093 REMARK 465 GLY B 1094 REMARK 465 GLY G 12 REMARK 465 GLY G 13 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 OG1 THR F 6 NH1 ARG F 8 1.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (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,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 MET A 962 CG - SD - CE ANGL. DEV. = -12.3 DEGREES REMARK 500 ARG A1039 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A1102 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 MET B 962 CA - CB - CG ANGL. DEV. = 11.8 DEGREES REMARK 500 ARG B1102 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG B1102 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG B1135 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 CYS B1170 N - CA - C ANGL. DEV. = -18.4 DEGREES REMARK 500 GLY B1171 N - CA - C ANGL. DEV. = -15.4 DEGREES REMARK 500 ARG B1188 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES 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 ASP A 925 105.57 -163.01 REMARK 500 ASP A 949 34.82 -84.91 REMARK 500 ASP A 978 -157.24 -92.15 REMARK 500 ILE A 992 -50.30 67.78 REMARK 500 ILE A1064 -61.67 -101.10 REMARK 500 ASN A1106 -162.52 -111.27 REMARK 500 ASP A1116 73.76 -109.41 REMARK 500 MET A1126 -92.49 -129.08 REMARK 500 ASP B 925 106.27 -162.97 REMARK 500 ASP B 949 36.46 -82.29 REMARK 500 ASP B 949 32.76 -79.57 REMARK 500 ASP B 978 -153.90 -102.88 REMARK 500 ILE B 992 -50.33 65.82 REMARK 500 ILE B1064 -62.90 -104.58 REMARK 500 ASN B1106 -164.71 -115.04 REMARK 500 ASP B1116 73.74 -112.38 REMARK 500 MET B1126 -93.90 -130.77 REMARK 500 SER B1187 78.75 -58.49 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 ZN A1202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 974 SG REMARK 620 2 CYS A 976 SG 104.4 REMARK 620 3 CYS A 980 SG 110.2 104.5 REMARK 620 4 CYS A 985 SG 112.4 106.7 117.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 974 SG REMARK 620 2 CYS A 987 SG 112.6 REMARK 620 3 CYS A1017 SG 108.3 112.7 REMARK 620 4 CYS A1021 SG 105.1 99.2 118.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 980 SG REMARK 620 2 CYS A1017 SG 109.0 REMARK 620 3 CYS A1023 SG 106.5 107.6 REMARK 620 4 CYS A1027 SG 111.7 108.4 113.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1204 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1115 SG REMARK 620 2 CYS A1168 SG 115.1 REMARK 620 3 CYS A1170 SG 109.8 103.5 REMARK 620 4 CYS A1175 SG 106.7 109.9 111.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 974 SG REMARK 620 2 CYS B 987 SG 112.7 REMARK 620 3 CYS B1017 SG 108.4 112.5 REMARK 620 4 CYS B1021 SG 106.0 100.4 116.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 974 SG REMARK 620 2 CYS B 976 SG 107.5 REMARK 620 3 CYS B 980 SG 107.5 106.8 REMARK 620 4 CYS B 985 SG 111.5 106.6 116.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 980 SG REMARK 620 2 CYS B1017 SG 110.3 REMARK 620 3 CYS B1023 SG 107.5 107.5 REMARK 620 4 CYS B1027 SG 112.8 106.1 112.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1204 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B1115 SG REMARK 620 2 CYS B1168 SG 114.0 REMARK 620 3 CYS B1170 SG 108.9 106.1 REMARK 620 4 CYS B1175 SG 105.5 109.0 113.4 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 1201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SAM A 1205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 1201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 1202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 1203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 1204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SAM B 1205 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5JJ0 RELATED DB: PDB REMARK 900 STRUCTURE OF G9A SET-DOMAIN WITH HISTONE H3K9M PEPTIDE AND EXCESS REMARK 900 SAH REMARK 900 RELATED ID: 5JIN RELATED DB: PDB REMARK 900 STRUCTURE OF G9A WITH H3K9MET MUTANT PEPTIDE PART OF THE SAME STUDY REMARK 900 RELATED ID: 5JIY RELATED DB: PDB REMARK 900 STRUCTURE OF G9A WITH H3K9NORLEU MUTANT PEPTIDE PART OF THE SAME REMARK 900 STUDY DBREF 5JHN A 916 1189 UNP Q96KQ7 EHMT2_HUMAN 882 1155 DBREF 5JHN F 3 13 PDB 5JHN 5JHN 3 13 DBREF 5JHN B 916 1189 UNP Q96KQ7 EHMT2_HUMAN 882 1155 DBREF 5JHN G 3 13 PDB 5JHN 5JHN 3 13 SEQRES 1 A 274 ILE ARG THR GLU LYS ILE ILE CYS ARG ASP VAL ALA ARG SEQRES 2 A 274 GLY TYR GLU ASN VAL PRO ILE PRO CYS VAL ASN GLY VAL SEQRES 3 A 274 ASP GLY GLU PRO CYS PRO GLU ASP TYR LYS TYR ILE SER SEQRES 4 A 274 GLU ASN CYS GLU THR SER THR MET ASN ILE ASP ARG ASN SEQRES 5 A 274 ILE THR HIS LEU GLN HIS CYS THR CYS VAL ASP ASP CYS SEQRES 6 A 274 SER SER SER ASN CYS LEU CYS GLY GLN LEU SER ILE ARG SEQRES 7 A 274 CYS TRP TYR ASP LYS ASP GLY ARG LEU LEU GLN GLU PHE SEQRES 8 A 274 ASN LYS ILE GLU PRO PRO LEU ILE PHE GLU CYS ASN GLN SEQRES 9 A 274 ALA CYS SER CYS TRP ARG ASN CYS LYS ASN ARG VAL VAL SEQRES 10 A 274 GLN SER GLY ILE LYS VAL ARG LEU GLN LEU TYR ARG THR SEQRES 11 A 274 ALA LYS MET GLY TRP GLY VAL ARG ALA LEU GLN THR ILE SEQRES 12 A 274 PRO GLN GLY THR PHE ILE CYS GLU TYR VAL GLY GLU LEU SEQRES 13 A 274 ILE SER ASP ALA GLU ALA ASP VAL ARG GLU ASP ASP SER SEQRES 14 A 274 TYR LEU PHE ASP LEU ASP ASN LYS ASP GLY GLU VAL TYR SEQRES 15 A 274 CYS ILE ASP ALA ARG TYR TYR GLY ASN ILE SER ARG PHE SEQRES 16 A 274 ILE ASN HIS LEU CYS ASP PRO ASN ILE ILE PRO VAL ARG SEQRES 17 A 274 VAL PHE MET LEU HIS GLN ASP LEU ARG PHE PRO ARG ILE SEQRES 18 A 274 ALA PHE PHE SER SER ARG ASP ILE ARG THR GLY GLU GLU SEQRES 19 A 274 LEU GLY PHE ASP TYR GLY ASP ARG PHE TRP ASP ILE LYS SEQRES 20 A 274 SER LYS TYR PHE THR CYS GLN CYS GLY SER GLU LYS CYS SEQRES 21 A 274 LYS HIS SER ALA GLU ALA ILE ALA LEU GLU GLN SER ARG SEQRES 22 A 274 LEU SEQRES 1 F 11 THR LYS GLN THR ALA ARG ALA SER THR GLY GLY SEQRES 1 B 274 ILE ARG THR GLU LYS ILE ILE CYS ARG ASP VAL ALA ARG SEQRES 2 B 274 GLY TYR GLU ASN VAL PRO ILE PRO CYS VAL ASN GLY VAL SEQRES 3 B 274 ASP GLY GLU PRO CYS PRO GLU ASP TYR LYS TYR ILE SER SEQRES 4 B 274 GLU ASN CYS GLU THR SER THR MET ASN ILE ASP ARG ASN SEQRES 5 B 274 ILE THR HIS LEU GLN HIS CYS THR CYS VAL ASP ASP CYS SEQRES 6 B 274 SER SER SER ASN CYS LEU CYS GLY GLN LEU SER ILE ARG SEQRES 7 B 274 CYS TRP TYR ASP LYS ASP GLY ARG LEU LEU GLN GLU PHE SEQRES 8 B 274 ASN LYS ILE GLU PRO PRO LEU ILE PHE GLU CYS ASN GLN SEQRES 9 B 274 ALA CYS SER CYS TRP ARG ASN CYS LYS ASN ARG VAL VAL SEQRES 10 B 274 GLN SER GLY ILE LYS VAL ARG LEU GLN LEU TYR ARG THR SEQRES 11 B 274 ALA LYS MET GLY TRP GLY VAL ARG ALA LEU GLN THR ILE SEQRES 12 B 274 PRO GLN GLY THR PHE ILE CYS GLU TYR VAL GLY GLU LEU SEQRES 13 B 274 ILE SER ASP ALA GLU ALA ASP VAL ARG GLU ASP ASP SER SEQRES 14 B 274 TYR LEU PHE ASP LEU ASP ASN LYS ASP GLY GLU VAL TYR SEQRES 15 B 274 CYS ILE ASP ALA ARG TYR TYR GLY ASN ILE SER ARG PHE SEQRES 16 B 274 ILE ASN HIS LEU CYS ASP PRO ASN ILE ILE PRO VAL ARG SEQRES 17 B 274 VAL PHE MET LEU HIS GLN ASP LEU ARG PHE PRO ARG ILE SEQRES 18 B 274 ALA PHE PHE SER SER ARG ASP ILE ARG THR GLY GLU GLU SEQRES 19 B 274 LEU GLY PHE ASP TYR GLY ASP ARG PHE TRP ASP ILE LYS SEQRES 20 B 274 SER LYS TYR PHE THR CYS GLN CYS GLY SER GLU LYS CYS SEQRES 21 B 274 LYS HIS SER ALA GLU ALA ILE ALA LEU GLU GLN SER ARG SEQRES 22 B 274 LEU SEQRES 1 G 11 THR LYS GLN THR ALA ARG ALA SER THR GLY GLY HET ZN A1201 1 HET ZN A1202 1 HET ZN A1203 1 HET ZN A1204 1 HET SAM A1205 27 HET ZN B1201 1 HET ZN B1202 1 HET ZN B1203 1 HET ZN B1204 1 HET SAM B1205 27 HETNAM ZN ZINC ION HETNAM SAM S-ADENOSYLMETHIONINE FORMUL 5 ZN 8(ZN 2+) FORMUL 9 SAM 2(C15 H22 N6 O5 S) FORMUL 15 HOH *154(H2 O) HELIX 1 AA1 ASN A 967 LEU A 971 5 5 HELIX 2 AA2 CYS A 985 LEU A 990 1 6 HELIX 3 AA3 VAL A 1031 GLY A 1035 5 5 HELIX 4 AA4 ASP A 1074 VAL A 1079 1 6 HELIX 5 AA5 ILE A 1107 ILE A 1111 5 5 HELIX 6 AA6 GLY A 1155 SER A 1163 1 9 HELIX 7 AA7 SER A 1178 SER A 1187 1 10 HELIX 8 AA8 ASN B 967 LEU B 971 5 5 HELIX 9 AA9 CYS B 985 LEU B 990 1 6 HELIX 10 AB1 VAL B 1031 GLY B 1035 5 5 HELIX 11 AB2 ASP B 1074 VAL B 1079 1 6 HELIX 12 AB3 ILE B 1107 ILE B 1111 5 5 HELIX 13 AB4 GLY B 1155 SER B 1163 1 9 HELIX 14 AB5 SER B 1178 SER B 1187 1 10 SHEET 1 AA1 4 LYS A 920 CYS A 923 0 SHEET 2 AA1 4 CYS A 937 ASN A 939 -1 O CYS A 937 N CYS A 923 SHEET 3 AA1 4 LEU A1040 ARG A1044 1 O LEU A1042 N VAL A 938 SHEET 4 AA1 4 TRP A1050 ALA A1054 -1 O GLY A1051 N TYR A1043 SHEET 1 AA2 4 LYS A 951 TYR A 952 0 SHEET 2 AA2 4 TYR A1097 GLY A1105 1 O TYR A1103 N LYS A 951 SHEET 3 AA2 4 GLY A1069 SER A1073 -1 N GLU A1070 O ASP A1100 SHEET 4 AA2 4 CYS A 957 GLU A 958 1 N CYS A 957 O LEU A1071 SHEET 1 AA3 3 LYS A 951 TYR A 952 0 SHEET 2 AA3 3 TYR A1097 GLY A1105 1 O TYR A1103 N LYS A 951 SHEET 3 AA3 3 LEU A1086 ASP A1088 -1 N PHE A1087 O ILE A1099 SHEET 1 AA4 4 ILE A1014 PHE A1015 0 SHEET 2 AA4 4 ILE A1119 PHE A1125 1 O ARG A1123 N ILE A1014 SHEET 3 AA4 4 ARG A1135 SER A1140 -1 O ALA A1137 N VAL A1122 SHEET 4 AA4 4 PHE A1063 TYR A1067 -1 N ILE A1064 O PHE A1138 SHEET 1 AA5 2 ASN A1112 HIS A1113 0 SHEET 2 AA5 2 GLY A1151 PHE A1152 1 O PHE A1152 N ASN A1112 SHEET 1 AA6 4 LYS B 920 CYS B 923 0 SHEET 2 AA6 4 CYS B 937 ASN B 939 -1 O CYS B 937 N ILE B 922 SHEET 3 AA6 4 LEU B1040 ARG B1044 1 O LEU B1042 N VAL B 938 SHEET 4 AA6 4 TRP B1050 ALA B1054 -1 O GLY B1051 N TYR B1043 SHEET 1 AA7 4 LYS B 951 TYR B 952 0 SHEET 2 AA7 4 TYR B1097 GLY B1105 1 O TYR B1103 N LYS B 951 SHEET 3 AA7 4 GLY B1069 SER B1073 -1 N GLU B1070 O ASP B1100 SHEET 4 AA7 4 CYS B 957 GLU B 958 1 N CYS B 957 O LEU B1071 SHEET 1 AA8 3 LYS B 951 TYR B 952 0 SHEET 2 AA8 3 TYR B1097 GLY B1105 1 O TYR B1103 N LYS B 951 SHEET 3 AA8 3 LEU B1086 LEU B1089 -1 N PHE B1087 O ILE B1099 SHEET 1 AA9 4 ILE B1014 PHE B1015 0 SHEET 2 AA9 4 ILE B1119 PHE B1125 1 O ARG B1123 N ILE B1014 SHEET 3 AA9 4 ARG B1135 SER B1140 -1 O ALA B1137 N VAL B1122 SHEET 4 AA9 4 PHE B1063 TYR B1067 -1 N CYS B1065 O PHE B1138 SHEET 1 AB1 2 ASN B1112 HIS B1113 0 SHEET 2 AB1 2 GLY B1151 PHE B1152 1 O PHE B1152 N ASN B1112 LINK SG CYS A 974 ZN ZN A1202 1555 1555 2.35 LINK SG CYS A 974 ZN ZN A1203 1555 1555 2.41 LINK SG CYS A 976 ZN ZN A1202 1555 1555 2.38 LINK SG CYS A 980 ZN ZN A1201 1555 1555 2.43 LINK SG CYS A 980 ZN ZN A1202 1555 1555 2.23 LINK SG CYS A 985 ZN ZN A1202 1555 1555 2.31 LINK SG CYS A 987 ZN ZN A1203 1555 1555 2.27 LINK SG CYS A1017 ZN ZN A1201 1555 1555 2.34 LINK SG CYS A1017 ZN ZN A1203 1555 1555 2.32 LINK SG CYS A1021 ZN ZN A1203 1555 1555 2.30 LINK SG CYS A1023 ZN ZN A1201 1555 1555 2.29 LINK SG CYS A1027 ZN ZN A1201 1555 1555 2.26 LINK SG CYS A1115 ZN ZN A1204 1555 1555 2.31 LINK SG CYS A1168 ZN ZN A1204 1555 1555 2.30 LINK SG CYS A1170 ZN ZN A1204 1555 1555 2.37 LINK SG CYS A1175 ZN ZN A1204 1555 1555 2.31 LINK SG CYS B 974 ZN ZN B1201 1555 1555 2.40 LINK SG CYS B 974 ZN ZN B1203 1555 1555 2.33 LINK SG CYS B 976 ZN ZN B1203 1555 1555 2.36 LINK SG CYS B 980 ZN ZN B1202 1555 1555 2.34 LINK SG CYS B 980 ZN ZN B1203 1555 1555 2.34 LINK SG CYS B 985 ZN ZN B1203 1555 1555 2.27 LINK SG CYS B 987 ZN ZN B1201 1555 1555 2.28 LINK SG CYS B1017 ZN ZN B1201 1555 1555 2.34 LINK SG CYS B1017 ZN ZN B1202 1555 1555 2.35 LINK SG CYS B1021 ZN ZN B1201 1555 1555 2.28 LINK SG CYS B1023 ZN ZN B1202 1555 1555 2.31 LINK SG CYS B1027 ZN ZN B1202 1555 1555 2.31 LINK SG CYS B1115 ZN ZN B1204 1555 1555 2.39 LINK SG CYS B1168 ZN ZN B1204 1555 1555 2.32 LINK SG CYS B1170 ZN ZN B1204 1555 1555 2.30 LINK SG CYS B1175 ZN ZN B1204 1555 1555 2.31 CISPEP 1 CYS B 1170 GLY B 1171 0 13.66 SITE 1 AC1 4 CYS A 980 CYS A1017 CYS A1023 CYS A1027 SITE 1 AC2 4 CYS A 974 CYS A 976 CYS A 980 CYS A 985 SITE 1 AC3 4 CYS A 974 CYS A 987 CYS A1017 CYS A1021 SITE 1 AC4 4 CYS A1115 CYS A1168 CYS A1170 CYS A1175 SITE 1 AC5 17 MET A1048 TRP A1050 SER A1084 TYR A1085 SITE 2 AC5 17 ARG A1109 PHE A1110 ASN A1112 HIS A1113 SITE 3 AC5 17 TYR A1154 PHE A1158 PHE A1166 THR A1167 SITE 4 AC5 17 CYS A1168 GLN A1169 HOH A1320 HOH A1351 SITE 5 AC5 17 HOH A1358 SITE 1 AC6 4 CYS B 974 CYS B 987 CYS B1017 CYS B1021 SITE 1 AC7 4 CYS B 980 CYS B1017 CYS B1023 CYS B1027 SITE 1 AC8 4 CYS B 974 CYS B 976 CYS B 980 CYS B 985 SITE 1 AC9 4 CYS B1115 CYS B1168 CYS B1170 CYS B1175 SITE 1 AD1 14 MET B1048 TRP B1050 SER B1084 TYR B1085 SITE 2 AD1 14 ARG B1109 PHE B1110 ASN B1112 HIS B1113 SITE 3 AD1 14 TYR B1154 PHE B1166 THR B1167 CYS B1168 SITE 4 AD1 14 GLN B1169 HOH B1361 CRYST1 56.782 78.270 73.121 90.00 90.34 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 0.017611 0.000000 0.000104 0.00000 SCALE2 0.000000 0.012776 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013676 0.00000