HEADER TRANSFERASE 27-NOV-17 5YVX TITLE CRYSTAL STRUCTURE OF SDG8 CW DOMAIN IN COMPLEX WITH H3K4ME1 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE ASHH2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ASH1 HOMOLOG 2,H3-K4-HMTASE,HISTONE H3-K36 METHYLTRANSFERASE COMPND 5 8,H3-K36-HMTASE 8,PROTEIN EARLY FLOWERING IN SHORT DAYS,PROTEIN COMPND 6 LAZARUS 2,PROTEIN SET DOMAIN GROUP 8; COMPND 7 EC: 2.1.1.43; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: H3K4ME1; COMPND 12 CHAIN: C; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: ASHH2, EFS, LAZ2, SDG8, SET8, AT1G77300, T14N5.15; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 11 ORGANISM_TAXID: 3702 KEYWDS SDG8, CW DOMAIN, H3K4ME1, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.LIU,Y.HUANG REVDAT 2 09-MAY-18 5YVX 1 JRNL REVDAT 1 14-MAR-18 5YVX 0 JRNL AUTH Y.LIU,Y.HUANG JRNL TITL UNCOVERING THE MECHANISTIC BASIS FOR SPECIFIC RECOGNITION OF JRNL TITL 2 MONOMETHYLATED H3K4 BY THE CW DOMAIN OFARABIDOPSISHISTONE JRNL TITL 3 METHYLTRANSFERASE SDG8. JRNL REF J. BIOL. CHEM. V. 293 6470 2018 JRNL REFN ESSN 1083-351X JRNL PMID 29496997 JRNL DOI 10.1074/JBC.RA117.001390 REMARK 2 REMARK 2 RESOLUTION. 1.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.510 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 19132 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1900 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 28.7658 - 3.8324 1.00 1243 138 0.1379 0.1482 REMARK 3 2 3.8324 - 3.0430 1.00 1252 131 0.1501 0.1838 REMARK 3 3 3.0430 - 2.6586 1.00 1243 136 0.1823 0.1648 REMARK 3 4 2.6586 - 2.4157 1.00 1254 139 0.1787 0.1723 REMARK 3 5 2.4157 - 2.2426 1.00 1236 141 0.1623 0.2097 REMARK 3 6 2.2426 - 2.1104 1.00 1249 142 0.1726 0.2083 REMARK 3 7 2.1104 - 2.0048 1.00 1240 135 0.1645 0.1770 REMARK 3 8 2.0048 - 1.9175 1.00 1226 140 0.1720 0.2130 REMARK 3 9 1.9175 - 1.8437 1.00 1247 126 0.1885 0.2044 REMARK 3 10 1.8437 - 1.7801 1.00 1279 143 0.1887 0.2220 REMARK 3 11 1.7801 - 1.7245 0.99 1198 136 0.2055 0.2374 REMARK 3 12 1.7245 - 1.6752 0.99 1240 144 0.2365 0.2489 REMARK 3 13 1.6752 - 1.6311 0.98 1222 132 0.2412 0.2697 REMARK 3 14 1.6311 - 1.5913 0.87 1103 117 0.2700 0.3191 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.870 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) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.007 536 REMARK 3 ANGLE : 0.991 718 REMARK 3 CHIRALITY : 0.045 76 REMARK 3 PLANARITY : 0.005 93 REMARK 3 DIHEDRAL : 15.524 199 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 5YVX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1300005913. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-AUG-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2824 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19136 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.590 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.65 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8.5, 30% PEG 3350, 30% REMARK 280 ISO-PROPANOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 14.62050 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 14.62050 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 14.62050 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1173 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 105 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 108 LIES ON A SPECIAL POSITION. 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 ARG C 8 REMARK 465 LYS C 9 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 GLU A 862 CG CD OE1 OE2 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 1132 O HOH A 1165 1.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 1157 O HOH A 1169 1556 1.84 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 A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 868 SG REMARK 620 2 CYS A 871 SG 109.8 REMARK 620 3 CYS A 893 SG 102.6 107.1 REMARK 620 4 CYS A 904 SG 107.7 111.3 117.9 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 Ligand residues MLZ C 4 through REMARK 800 GLN C 5 bound to THR C 3 DBREF 5YVX A 862 921 UNP Q2LAE1 ASHH2_ARATH 862 921 DBREF 5YVX C 1 9 PDB 5YVX 5YVX 1 9 SEQADV 5YVX ALA A 917 UNP Q2LAE1 GLU 917 ENGINEERED MUTATION SEQRES 1 A 60 GLU SER ALA TRP VAL ARG CYS ASP ASP CYS PHE LYS TRP SEQRES 2 A 60 ARG ARG ILE PRO ALA SER VAL VAL GLY SER ILE ASP GLU SEQRES 3 A 60 SER SER ARG TRP ILE CYS MET ASN ASN SER ASP LYS ARG SEQRES 4 A 60 PHE ALA ASP CYS SER LYS SER GLN GLU MET SER ASN GLU SEQRES 5 A 60 GLU ILE ASN ALA GLU LEU GLY ILE SEQRES 1 C 9 ALA ARG THR MLZ GLN THR ALA ARG LYS HET MLZ C 4 10 HET ZN A1001 1 HETNAM MLZ N-METHYL-LYSINE HETNAM ZN ZINC ION FORMUL 2 MLZ C7 H16 N2 O2 FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *84(H2 O) HELIX 1 AA1 ALA A 879 GLY A 883 1 5 HELIX 2 AA2 ILE A 892 ASN A 896 5 5 HELIX 3 AA3 SER A 911 GLY A 920 1 10 SHEET 1 AA1 3 TRP A 874 PRO A 878 0 SHEET 2 AA1 3 SER A 863 ARG A 867 -1 N ALA A 864 O ILE A 877 SHEET 3 AA1 3 THR C 3 MLZ C 4 -1 O MLZ C 4 N TRP A 865 LINK SG CYS A 868 ZN L ZN A1001 1555 1555 2.36 LINK SG CYS A 871 ZN L ZN A1001 1555 1555 2.31 LINK SG CYS A 893 ZN L ZN A1001 1555 1555 2.34 LINK SG CYS A 904 ZN L ZN A1001 1555 1555 2.31 LINK C THR C 3 N MLZ C 4 1555 1555 1.33 LINK C MLZ C 4 N GLN C 5 1555 1555 1.33 SITE 1 AC1 4 CYS A 868 CYS A 871 CYS A 893 CYS A 904 SITE 1 AC2 11 ALA A 864 TRP A 865 VAL A 882 ASN A 916 SITE 2 AC2 11 LEU A 919 THR C 3 THR C 6 ALA C 7 SITE 3 AC2 11 HOH C 102 HOH C 103 HOH C 106 CRYST1 66.421 66.421 29.241 90.00 90.00 120.00 P 63 6 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 0.015055 0.008692 0.000000 0.00000 SCALE2 0.000000 0.017385 0.000000 0.00000 SCALE3 0.000000 0.000000 0.034199 0.00000