HEADER TRANSFERASE 13-JUL-11 3SWC TITLE GLP (G9A-LIKE PROTEIN) SET DOMAIN IN COMPLEX WITH DNMT3AK44ME2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE EHMT1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 982-1266; COMPND 5 SYNONYM: EUCHROMATIC HISTONE-LYSINE N-METHYLTRANSFERASE 1, EU- COMPND 6 HMTASE1, G9A-LIKE PROTEIN 1, GLP, GLP1, HISTONE H3-K9 COMPND 7 METHYLTRANSFERASE 5, H3-K9-HMTASE 5, LYSINE N-METHYLTRANSFERASE 1D; COMPND 8 EC: 2.1.1.-, 2.1.1.43; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: DNA (CYTOSINE-5)-METHYLTRANSFERASE 3A; COMPND 12 CHAIN: P, Q; COMPND 13 FRAGMENT: UNP RESIDUES 39-50; COMPND 14 SYNONYM: DNMT3A, DNA METHYLTRANSFERASE MMUIIIA, DNA MTASE MMUIIIA, COMPND 15 M.MMUIIIA; COMPND 16 EC: 2.1.1.37; COMPND 17 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: EHMT1, EUHMTASE1, GLP, KIAA1876, KMT1D; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PXC681; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 13 ORGANISM_COMMON: MOUSE; SOURCE 14 ORGANISM_TAXID: 10090 KEYWDS EPIGENETICS, NON-HISTONE LYSINE METHYLATION, SET DOMAIN, PROTEIN KEYWDS 2 LYSINE METHYLTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.CHANG,J.R.HORTON,X.ZHANG,X.CHENG REVDAT 1 30-NOV-11 3SWC 0 JRNL AUTH Y.CHANG,L.SUN,K.KOKURA,J.R.HORTON,M.FUKUDA,A.ESPEJO,V.IZUMI, JRNL AUTH 2 J.M.KOOMEN,M.T.BEDFORD,X.ZHANG,Y.SHINKAI,J.FANG,X.CHENG JRNL TITL MPP8 MEDIATES THE INTERACTIONS BETWEEN DNA METHYLTRANSFERASE JRNL TITL 2 DNMT3A AND H3K9 METHYLTRANSFERASE GLP/G9A. JRNL REF NAT COMMUN V. 2 533 2011 JRNL REFN ESSN 2041-1723 JRNL PMID 22086334 JRNL DOI 10.1038/NCOMMS1549 REMARK 2 REMARK 2 RESOLUTION. 2.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6_289) 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) : 2.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.040 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 28620 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.870 REMARK 3 FREE R VALUE TEST SET COUNT : 1967 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 40.7872 - 5.0206 0.98 2925 215 0.1740 0.1829 REMARK 3 2 5.0206 - 3.9861 1.00 2838 210 0.1503 0.1843 REMARK 3 3 3.9861 - 3.4826 0.99 2812 199 0.1667 0.2168 REMARK 3 4 3.4826 - 3.1643 1.00 2793 213 0.1963 0.2310 REMARK 3 5 3.1643 - 2.9375 0.99 2747 201 0.2055 0.2711 REMARK 3 6 2.9375 - 2.7644 0.97 2688 200 0.2062 0.2743 REMARK 3 7 2.7644 - 2.6260 0.94 2593 202 0.2023 0.2272 REMARK 3 8 2.6260 - 2.5117 0.92 2544 181 0.1944 0.2346 REMARK 3 9 2.5117 - 2.4150 0.91 2529 186 0.2105 0.2782 REMARK 3 10 2.4150 - 2.3317 0.80 2184 160 0.2169 0.3090 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 : 0.35 REMARK 3 B_SOL : 31.41 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.95210 REMARK 3 B22 (A**2) : 5.03360 REMARK 3 B33 (A**2) : -5.98570 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 : 0.008 4458 REMARK 3 ANGLE : 1.137 6040 REMARK 3 CHIRALITY : 0.075 627 REMARK 3 PLANARITY : 0.005 802 REMARK 3 DIHEDRAL : 17.553 1650 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 3SWC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JUL-11. REMARK 100 THE RCSB ID CODE IS RCSB066733. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29318 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.330 REMARK 200 RESOLUTION RANGE LOW (A) : 40.780 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : 8.70 REMARK 200 R MERGE FOR SHELL (I) : 0.40600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB 3MO5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, 16% POLYETHYLENE GLYCOL REMARK 280 4000 AND 8% ISOPROPANOL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 289K 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 40.04500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.70000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.11000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.70000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.04500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.11000 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, 3 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: 1310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P 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: 1420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, Q 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: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P, B, Q 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 ASN A 951 REMARK 465 SER A 952 REMARK 465 GLN A 953 REMARK 465 VAL A 954 REMARK 465 TRP A 955 REMARK 465 SER A 956 REMARK 465 ALA A 957 REMARK 465 LEU A 958 REMARK 465 GLN A 959 REMARK 465 MET A 960 REMARK 465 SER A 961 REMARK 465 LYS A 962 REMARK 465 ALA A 963 REMARK 465 LEU A 964 REMARK 465 GLN A 965 REMARK 465 ASP A 966 REMARK 465 SER A 967 REMARK 465 ALA A 968 REMARK 465 PRO A 969 REMARK 465 ASP A 970 REMARK 465 ARG A 971 REMARK 465 PRO A 972 REMARK 465 SER A 973 REMARK 465 PRO A 974 REMARK 465 SER P 39 REMARK 465 ALA P 40 REMARK 465 ARG P 50 REMARK 465 ASN B 951 REMARK 465 SER B 952 REMARK 465 GLN B 953 REMARK 465 VAL B 954 REMARK 465 TRP B 955 REMARK 465 SER B 956 REMARK 465 ALA B 957 REMARK 465 LEU B 958 REMARK 465 GLN B 959 REMARK 465 MET B 960 REMARK 465 SER B 961 REMARK 465 LYS B 962 REMARK 465 ALA B 963 REMARK 465 LEU B 964 REMARK 465 GLN B 965 REMARK 465 ASP B 966 REMARK 465 SER B 967 REMARK 465 ALA B 968 REMARK 465 PRO B 969 REMARK 465 ASP B 970 REMARK 465 ARG B 971 REMARK 465 PRO B 972 REMARK 465 SER B 973 REMARK 465 PRO B 974 REMARK 465 SER Q 39 REMARK 465 ALA Q 40 REMARK 465 THR Q 41 REMARK 465 ARG Q 50 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 VAL A 975 CG1 CG2 REMARK 470 ARG A 981 CG CD NE CZ NH1 NH2 REMARK 470 ARG A1103 CG CD NE CZ NH1 NH2 REMARK 470 ASP A1104 CG OD1 OD2 REMARK 470 GLU A1138 CG CD OE1 OE2 REMARK 470 LYS A1221 CG CD CE NZ REMARK 470 LYS A1231 CG CD CE NZ REMARK 470 ARG P 43 CG CD NE CZ NH1 NH2 REMARK 470 VAL B 975 CG1 CG2 REMARK 470 ARG B 981 CG CD NE CZ NH1 NH2 REMARK 470 ASP B1104 CG OD1 OD2 REMARK 470 GLU B1138 CG CD OE1 OE2 REMARK 470 LYS B1149 CG CD CE NZ REMARK 470 ASP B1150 CG OD1 OD2 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 O HOH A 10 O HOH A 166 2.09 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 GLU A 976 -164.80 -122.56 REMARK 500 VAL A 979 4.08 -60.56 REMARK 500 SER A 980 144.97 -172.10 REMARK 500 ASP A 982 106.21 -173.55 REMARK 500 ASP A 999 -155.42 -145.34 REMARK 500 SER A1017 115.15 147.97 REMARK 500 ASN A1024 109.55 -59.89 REMARK 500 ASP A1035 -151.85 -117.78 REMARK 500 MET A1049 -66.36 87.17 REMARK 500 ASN A1086 45.35 -86.87 REMARK 500 VAL A1088 -64.00 -140.46 REMARK 500 ASN A1163 -167.62 -109.67 REMARK 500 GLU A1173 73.97 -111.63 REMARK 500 MET A1183 -87.38 -132.07 REMARK 500 ALA P 42 -111.40 78.07 REMARK 500 ARG P 43 -142.14 -170.65 REMARK 500 VAL P 45 46.47 -90.52 REMARK 500 PRO P 48 -162.76 -117.64 REMARK 500 GLU B 976 97.69 -60.15 REMARK 500 ILE B 978 96.35 -69.22 REMARK 500 SER B 980 141.32 -170.90 REMARK 500 ASP B 982 96.09 -171.21 REMARK 500 ALA B 997 27.30 -145.17 REMARK 500 ASP B 999 -159.46 -167.07 REMARK 500 GLU B1001 124.79 -39.98 REMARK 500 ASN B1006 38.77 -93.27 REMARK 500 THR B1016 -80.74 -104.83 REMARK 500 ASP B1035 -150.38 -100.08 REMARK 500 MET B1049 -47.26 81.21 REMARK 500 ASN B1086 51.44 -93.97 REMARK 500 VAL B1088 -60.70 -135.61 REMARK 500 ASP B1147 100.69 19.63 REMARK 500 ASN B1163 -161.85 -108.68 REMARK 500 MET B1183 -96.57 -134.55 REMARK 500 ARG B1199 -177.79 -174.07 REMARK 500 HIS B1234 22.17 -140.89 REMARK 500 MLY Q 44 99.36 85.74 REMARK 500 PRO Q 48 86.51 -14.20 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 ASP B1147 24.7 L L OUTSIDE RANGE 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 A 304 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1225 SG REMARK 620 2 CYS A1227 SG 108.7 REMARK 620 3 CYS A1172 SG 116.7 107.9 REMARK 620 4 CYS A1232 SG 103.2 111.5 108.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 305 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B1044 SG REMARK 620 2 CYS B1074 SG 115.8 REMARK 620 3 CYS B1078 SG 95.5 121.9 REMARK 620 4 CYS B1031 SG 112.7 108.1 101.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1074 SG REMARK 620 2 CYS A1044 SG 116.9 REMARK 620 3 CYS A1078 SG 126.0 94.9 REMARK 620 4 CYS A1031 SG 102.7 115.7 100.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1074 SG REMARK 620 2 CYS A1084 SG 109.3 REMARK 620 3 CYS A1080 SG 105.7 120.2 REMARK 620 4 CYS A1037 SG 104.4 110.0 106.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 308 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B1172 SG REMARK 620 2 CYS B1227 SG 112.7 REMARK 620 3 CYS B1225 SG 120.4 103.5 REMARK 620 4 CYS B1232 SG 103.6 115.4 101.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 306 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B1084 SG REMARK 620 2 CYS B1074 SG 108.0 REMARK 620 3 CYS B1080 SG 118.7 104.0 REMARK 620 4 CYS B1037 SG 111.2 112.3 102.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 307 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B1042 SG REMARK 620 2 CYS B1037 SG 121.6 REMARK 620 3 CYS B1031 SG 110.1 109.8 REMARK 620 4 CYS B1033 SG 105.4 102.7 105.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1037 SG REMARK 620 2 CYS A1042 SG 119.2 REMARK 620 3 CYS A1033 SG 103.5 106.9 REMARK 620 4 CYS A1031 SG 106.8 112.2 107.4 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3SW9 RELATED DB: PDB REMARK 900 GLP SET DOMAIN IN COMPLEX WITH DNMT3AK44ME0 PEPTIDE REMARK 900 RELATED ID: 3SVM RELATED DB: PDB DBREF 3SWC A 951 1235 UNP Q9H9B1 EHMT1_HUMAN 982 1266 DBREF 3SWC P 39 50 UNP O88508 DNM3A_MOUSE 39 50 DBREF 3SWC B 951 1235 UNP Q9H9B1 EHMT1_HUMAN 982 1266 DBREF 3SWC Q 39 50 UNP O88508 DNM3A_MOUSE 39 50 SEQRES 1 A 285 ASN SER GLN VAL TRP SER ALA LEU GLN MET SER LYS ALA SEQRES 2 A 285 LEU GLN ASP SER ALA PRO ASP ARG PRO SER PRO VAL GLU SEQRES 3 A 285 ARG ILE VAL SER ARG ASP ILE ALA ARG GLY TYR GLU ARG SEQRES 4 A 285 ILE PRO ILE PRO CYS VAL ASN ALA VAL ASP SER GLU PRO SEQRES 5 A 285 CYS PRO SER ASN TYR LYS TYR VAL SER GLN ASN CYS VAL SEQRES 6 A 285 THR SER PRO MET ASN ILE ASP ARG ASN ILE THR HIS LEU SEQRES 7 A 285 GLN TYR CYS VAL CYS ILE ASP ASP CYS SER SER SER ASN SEQRES 8 A 285 CYS MET CYS GLY GLN LEU SER MET ARG CYS TRP TYR ASP SEQRES 9 A 285 LYS ASP GLY ARG LEU LEU PRO GLU PHE ASN MET ALA GLU SEQRES 10 A 285 PRO PRO LEU ILE PHE GLU CYS ASN HIS ALA CYS SER CYS SEQRES 11 A 285 TRP ARG ASN CYS ARG ASN ARG VAL VAL GLN ASN GLY LEU SEQRES 12 A 285 ARG ALA ARG LEU GLN LEU TYR ARG THR ARG ASP MET GLY SEQRES 13 A 285 TRP GLY VAL ARG SER LEU GLN ASP ILE PRO PRO GLY THR SEQRES 14 A 285 PHE VAL CYS GLU TYR VAL GLY GLU LEU ILE SER ASP SER SEQRES 15 A 285 GLU ALA ASP VAL ARG GLU GLU ASP SER TYR LEU PHE ASP SEQRES 16 A 285 LEU ASP ASN LYS ASP GLY GLU VAL TYR CYS ILE ASP ALA SEQRES 17 A 285 ARG PHE TYR GLY ASN VAL SER ARG PHE ILE ASN HIS HIS SEQRES 18 A 285 CYS GLU PRO ASN LEU VAL PRO VAL ARG VAL PHE MET ALA SEQRES 19 A 285 HIS GLN ASP LEU ARG PHE PRO ARG ILE ALA PHE PHE SER SEQRES 20 A 285 THR ARG LEU ILE GLU ALA GLY GLU GLN LEU GLY PHE ASP SEQRES 21 A 285 TYR GLY GLU ARG PHE TRP ASP ILE LYS GLY LYS LEU PHE SEQRES 22 A 285 SER CYS ARG CYS GLY SER PRO LYS CYS ARG HIS SER SEQRES 1 P 12 SER ALA THR ALA ARG MLY VAL GLY ARG PRO GLY ARG SEQRES 1 B 285 ASN SER GLN VAL TRP SER ALA LEU GLN MET SER LYS ALA SEQRES 2 B 285 LEU GLN ASP SER ALA PRO ASP ARG PRO SER PRO VAL GLU SEQRES 3 B 285 ARG ILE VAL SER ARG ASP ILE ALA ARG GLY TYR GLU ARG SEQRES 4 B 285 ILE PRO ILE PRO CYS VAL ASN ALA VAL ASP SER GLU PRO SEQRES 5 B 285 CYS PRO SER ASN TYR LYS TYR VAL SER GLN ASN CYS VAL SEQRES 6 B 285 THR SER PRO MET ASN ILE ASP ARG ASN ILE THR HIS LEU SEQRES 7 B 285 GLN TYR CYS VAL CYS ILE ASP ASP CYS SER SER SER ASN SEQRES 8 B 285 CYS MET CYS GLY GLN LEU SER MET ARG CYS TRP TYR ASP SEQRES 9 B 285 LYS ASP GLY ARG LEU LEU PRO GLU PHE ASN MET ALA GLU SEQRES 10 B 285 PRO PRO LEU ILE PHE GLU CYS ASN HIS ALA CYS SER CYS SEQRES 11 B 285 TRP ARG ASN CYS ARG ASN ARG VAL VAL GLN ASN GLY LEU SEQRES 12 B 285 ARG ALA ARG LEU GLN LEU TYR ARG THR ARG ASP MET GLY SEQRES 13 B 285 TRP GLY VAL ARG SER LEU GLN ASP ILE PRO PRO GLY THR SEQRES 14 B 285 PHE VAL CYS GLU TYR VAL GLY GLU LEU ILE SER ASP SER SEQRES 15 B 285 GLU ALA ASP VAL ARG GLU GLU ASP SER TYR LEU PHE ASP SEQRES 16 B 285 LEU ASP ASN LYS ASP GLY GLU VAL TYR CYS ILE ASP ALA SEQRES 17 B 285 ARG PHE TYR GLY ASN VAL SER ARG PHE ILE ASN HIS HIS SEQRES 18 B 285 CYS GLU PRO ASN LEU VAL PRO VAL ARG VAL PHE MET ALA SEQRES 19 B 285 HIS GLN ASP LEU ARG PHE PRO ARG ILE ALA PHE PHE SER SEQRES 20 B 285 THR ARG LEU ILE GLU ALA GLY GLU GLN LEU GLY PHE ASP SEQRES 21 B 285 TYR GLY GLU ARG PHE TRP ASP ILE LYS GLY LYS LEU PHE SEQRES 22 B 285 SER CYS ARG CYS GLY SER PRO LYS CYS ARG HIS SER SEQRES 1 Q 12 SER ALA THR ALA ARG MLY VAL GLY ARG PRO GLY ARG MODRES 3SWC MLY P 44 LYS N-DIMETHYL-LYSINE MODRES 3SWC MLY Q 44 LYS N-DIMETHYL-LYSINE HET MLY P 44 11 HET MLY Q 44 11 HET ZN A 301 1 HET ZN A 302 1 HET ZN A 303 1 HET ZN A 304 1 HET SAH A 202 26 HET ZN B 305 1 HET ZN B 306 1 HET ZN B 307 1 HET ZN B 308 1 HET SAH B 201 26 HETNAM MLY N-DIMETHYL-LYSINE HETNAM ZN ZINC ION HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE FORMUL 2 MLY 2(C8 H18 N2 O2) FORMUL 5 ZN 8(ZN 2+) FORMUL 9 SAH 2(C14 H20 N6 O5 S) FORMUL 15 HOH *170(H2 O) HELIX 1 1 ASN A 1024 LEU A 1028 5 5 HELIX 2 2 CYS A 1042 SER A 1048 1 7 HELIX 3 3 VAL A 1088 GLY A 1092 5 5 HELIX 4 4 ASP A 1131 VAL A 1136 1 6 HELIX 5 5 VAL A 1164 ILE A 1168 5 5 HELIX 6 6 GLY A 1212 GLY A 1220 1 9 HELIX 7 7 ASN B 1024 LEU B 1028 5 5 HELIX 8 8 CYS B 1042 SER B 1048 1 7 HELIX 9 9 VAL B 1088 GLY B 1092 5 5 HELIX 10 10 SER B 1130 VAL B 1136 1 7 HELIX 11 11 VAL B 1164 ILE B 1168 5 5 HELIX 12 12 GLY B 1212 GLY B 1220 1 9 SHEET 1 A 3 CYS A 994 VAL A 995 0 SHEET 2 A 3 LEU A1097 ARG A1101 1 O LEU A1099 N VAL A 995 SHEET 3 A 3 TRP A1107 SER A1111 -1 O ARG A1110 N GLN A1098 SHEET 1 B 3 LYS A1008 TYR A1009 0 SHEET 2 B 3 VAL A1153 GLY A1162 1 O PHE A1160 N LYS A1008 SHEET 3 B 3 GLY A1126 SER A1130 -1 N ILE A1129 O CYS A1155 SHEET 1 C 3 LYS A1008 TYR A1009 0 SHEET 2 C 3 VAL A1153 GLY A1162 1 O PHE A1160 N LYS A1008 SHEET 3 C 3 LEU A1143 ASP A1147 -1 N LEU A1146 O TYR A1154 SHEET 1 D 4 ILE A1071 PHE A1072 0 SHEET 2 D 4 LEU A1176 PHE A1182 1 O PHE A1182 N ILE A1071 SHEET 3 D 4 ARG A1192 SER A1197 -1 O ALA A1194 N VAL A1179 SHEET 4 D 4 PHE A1120 TYR A1124 -1 N CYS A1122 O PHE A1195 SHEET 1 E 2 ASN A1169 HIS A1170 0 SHEET 2 E 2 GLY A1208 PHE A1209 1 O PHE A1209 N ASN A1169 SHEET 1 F 4 ARG B 977 SER B 980 0 SHEET 2 F 4 CYS B 994 ASN B 996 -1 O CYS B 994 N SER B 980 SHEET 3 F 4 LEU B1097 ARG B1101 1 O LEU B1099 N VAL B 995 SHEET 4 F 4 TRP B1107 SER B1111 -1 O GLY B1108 N TYR B1100 SHEET 1 G 4 LYS B1008 TYR B1009 0 SHEET 2 G 4 CYS B1155 GLY B1162 1 O PHE B1160 N LYS B1008 SHEET 3 G 4 GLY B1126 ILE B1129 -1 N ILE B1129 O CYS B1155 SHEET 4 G 4 CYS B1014 VAL B1015 1 N CYS B1014 O LEU B1128 SHEET 1 H 3 LYS B1008 TYR B1009 0 SHEET 2 H 3 CYS B1155 GLY B1162 1 O PHE B1160 N LYS B1008 SHEET 3 H 3 LEU B1143 ASP B1145 -1 N PHE B1144 O ILE B1156 SHEET 1 I 4 ILE B1071 PHE B1072 0 SHEET 2 I 4 LEU B1176 PHE B1182 1 O PHE B1182 N ILE B1071 SHEET 3 I 4 ARG B1192 SER B1197 -1 O ALA B1194 N VAL B1179 SHEET 4 I 4 PHE B1120 GLU B1123 -1 N CYS B1122 O PHE B1195 SHEET 1 J 2 ASN B1169 HIS B1170 0 SHEET 2 J 2 GLY B1208 PHE B1209 1 O PHE B1209 N ASN B1169 LINK C MLY P 44 N VAL P 45 1555 1555 1.32 LINK C ARG Q 43 N MLY Q 44 1555 1555 1.33 LINK C MLY Q 44 N VAL Q 45 1555 1555 1.32 LINK SG CYS A1225 ZN ZN A 304 1555 1555 2.20 LINK SG CYS B1044 ZN ZN B 305 1555 1555 2.20 LINK SG CYS A1074 ZN ZN A 301 1555 1555 2.22 LINK SG CYS A1074 ZN ZN A 302 1555 1555 2.25 LINK SG CYS B1074 ZN ZN B 305 1555 1555 2.26 LINK SG CYS A1084 ZN ZN A 302 1555 1555 2.26 LINK SG CYS A1044 ZN ZN A 301 1555 1555 2.27 LINK SG CYS B1172 ZN ZN B 308 1555 1555 2.28 LINK SG CYS A1080 ZN ZN A 302 1555 1555 2.28 LINK SG CYS B1084 ZN ZN B 306 1555 1555 2.28 LINK SG CYS A1078 ZN ZN A 301 1555 1555 2.29 LINK SG CYS B1074 ZN ZN B 306 1555 1555 2.31 LINK SG CYS B1042 ZN ZN B 307 1555 1555 2.31 LINK SG CYS A1037 ZN ZN A 303 1555 1555 2.31 LINK SG CYS B1037 ZN ZN B 307 1555 1555 2.32 LINK SG CYS B1227 ZN ZN B 308 1555 1555 2.33 LINK SG CYS B1225 ZN ZN B 308 1555 1555 2.34 LINK SG CYS B1080 ZN ZN B 306 1555 1555 2.35 LINK SG CYS A1042 ZN ZN A 303 1555 1555 2.36 LINK SG CYS B1078 ZN ZN B 305 1555 1555 2.37 LINK SG CYS A1033 ZN ZN A 303 1555 1555 2.38 LINK SG CYS A1227 ZN ZN A 304 1555 1555 2.40 LINK SG CYS B1031 ZN ZN B 307 1555 1555 2.40 LINK SG CYS A1031 ZN ZN A 303 1555 1555 2.40 LINK SG CYS B1031 ZN ZN B 305 1555 1555 2.42 LINK SG CYS B1037 ZN ZN B 306 1555 1555 2.43 LINK SG CYS A1172 ZN ZN A 304 1555 1555 2.43 LINK SG CYS B1033 ZN ZN B 307 1555 1555 2.44 LINK SG CYS A1031 ZN ZN A 301 1555 1555 2.45 LINK SG CYS B1232 ZN ZN B 308 1555 1555 2.47 LINK SG CYS A1037 ZN ZN A 302 1555 1555 2.48 LINK SG CYS A1232 ZN ZN A 304 1555 1555 2.51 LINK C ARG P 43 N MLY P 44 1555 1555 1.33 CISPEP 1 ARG P 47 PRO P 48 0 -0.56 SITE 1 AC1 4 CYS A1031 CYS A1044 CYS A1074 CYS A1078 SITE 1 AC2 4 CYS A1037 CYS A1074 CYS A1080 CYS A1084 SITE 1 AC3 4 CYS A1031 CYS A1033 CYS A1037 CYS A1042 SITE 1 AC4 4 CYS A1172 CYS A1225 CYS A1227 CYS A1232 SITE 1 AC5 13 MET A1105 TRP A1107 SER A1141 TYR A1142 SITE 2 AC5 13 ARG A1166 ASN A1169 HIS A1170 TYR A1211 SITE 3 AC5 13 PHE A1223 SER A1224 CYS A1225 ARG A1226 SITE 4 AC5 13 ARG P 47 SITE 1 AC6 4 CYS B1031 CYS B1044 CYS B1074 CYS B1078 SITE 1 AC7 5 ZN B 307 CYS B1037 CYS B1074 CYS B1080 SITE 2 AC7 5 CYS B1084 SITE 1 AC8 5 ZN B 306 CYS B1031 CYS B1033 CYS B1037 SITE 2 AC8 5 CYS B1042 SITE 1 AC9 4 CYS B1172 CYS B1225 CYS B1227 CYS B1232 SITE 1 BC1 15 MET B1105 GLY B1106 TRP B1107 SER B1141 SITE 2 BC1 15 TYR B1142 ARG B1166 PHE B1167 ASN B1169 SITE 3 BC1 15 HIS B1170 TYR B1211 PHE B1215 PHE B1223 SITE 4 BC1 15 CYS B1225 ARG B1226 ARG Q 47 CRYST1 80.090 90.220 95.400 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 0.012486 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011084 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010482 0.00000