HEADER TRANSCRIPTION 02-MAY-11 3RSN TITLE CRYSTAL STRUCTURE OF THE N-TERMINAL REGION OF HUMAN ASH2L COMPND MOL_ID: 1; COMPND 2 MOLECULE: SET1/ASH2 HISTONE METHYLTRANSFERASE COMPLEX SUBUNIT ASH2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ASH2L N-TERMINAL DOMAIN, UNP RESIDUES 96-271; COMPND 5 SYNONYM: ASH2-LIKE PROTEIN; COMPND 6 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: ASH2L, ASH2L1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS PHD DOMAIN, WINGED HELIX DOMAIN, HISTONE METHYLTRANSFERASE, DNA KEYWDS 2 BINDING, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR Y.CHEN,B.WAN,K.C.WANG,F.CAO,Y.YANG,A.PROTACIO,Y.DOU,H.Y.CHANG,M.LEI REVDAT 2 14-DEC-11 3RSN 1 JRNL VERSN REVDAT 1 22-JUN-11 3RSN 0 JRNL AUTH Y.CHEN,B.WAN,K.C.WANG,F.CAO,Y.YANG,A.PROTACIO,Y.DOU, JRNL AUTH 2 H.Y.CHANG,M.LEI JRNL TITL CRYSTAL STRUCTURE OF THE N-TERMINAL REGION OF HUMAN ASH2L JRNL TITL 2 SHOWS A WINGED-HELIX MOTIF INVOLVED IN DNA BINDING. JRNL REF EMBO REP. V. 12 797 2011 JRNL REFN ISSN 1469-221X JRNL PMID 21660059 JRNL DOI 10.1038/EMBOR.2011.101 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.110 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 14752 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.520 REMARK 3 FREE R VALUE TEST SET COUNT : 2554 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 34.0610 - 4.5211 0.99 2446 211 0.1826 0.2032 REMARK 3 2 4.5211 - 3.5898 0.99 2403 257 0.1788 0.2042 REMARK 3 3 3.5898 - 3.1364 1.00 2487 235 0.2051 0.2503 REMARK 3 4 3.1364 - 2.8498 1.00 2464 272 0.2337 0.2958 REMARK 3 5 2.8498 - 2.6456 1.00 2403 259 0.2528 0.2857 REMARK 3 6 2.6456 - 2.4897 1.00 2416 284 0.2611 0.3241 REMARK 3 7 2.4897 - 2.3650 1.00 2456 245 0.2668 0.3308 REMARK 3 8 2.3650 - 2.2621 1.00 2425 260 0.2587 0.3170 REMARK 3 9 2.2621 - 2.1750 1.00 2401 282 0.2732 0.3249 REMARK 3 10 2.1750 - 2.1000 0.96 2367 249 0.3228 0.4175 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.95 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 41.29 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.310 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) : 2.57710 REMARK 3 B22 (A**2) : 2.57710 REMARK 3 B33 (A**2) : -5.15420 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 : 0.011 1399 REMARK 3 ANGLE : 1.117 1856 REMARK 3 CHIRALITY : 0.084 193 REMARK 3 PLANARITY : 0.005 242 REMARK 3 DIHEDRAL : 14.599 513 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 3RSN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAY-11. REMARK 100 THE RCSB ID CODE IS RCSB065327. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 100 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 : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : C(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR 300 CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14752 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 19.000 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 73.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 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: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS-HCL PH8.5, 20% PEG8000, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 55.17300 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 110.34600 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 110.34600 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 55.17300 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 SER A 1 REMARK 465 ASP A 2 REMARK 465 THR A 3 REMARK 465 GLN A 4 REMARK 465 ALA A 5 REMARK 465 GLY A 6 REMARK 465 SER A 7 REMARK 465 VAL A 8 REMARK 465 ASP A 9 REMARK 465 GLU A 10 REMARK 465 ASN A 176 REMARK 465 GLN A 177 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 ASN A 12 4.55 58.87 REMARK 500 GLN A 15 72.24 -116.90 REMARK 500 PHE A 45 31.93 73.36 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 200 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 56 SG REMARK 620 2 CYS A 26 SG 104.9 REMARK 620 3 CYS A 53 SG 100.9 118.9 REMARK 620 4 CYS A 23 SG 114.0 105.8 112.4 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 200 DBREF 3RSN A 2 177 UNP Q9UBL3 ASH2L_HUMAN 96 271 SEQADV 3RSN SER A 1 UNP Q9UBL3 EXPRESSION TAG SEQRES 1 A 177 SER ASP THR GLN ALA GLY SER VAL ASP GLU GLU ASN GLY SEQRES 2 A 177 ARG GLN LEU GLY GLU VAL GLU LEU GLN CYS GLY ILE CYS SEQRES 3 A 177 THR LYS TRP PHE THR ALA ASP THR PHE GLY ILE ASP THR SEQRES 4 A 177 SER SER CYS LEU PRO PHE MSE THR ASN TYR SER PHE HIS SEQRES 5 A 177 CYS ASN VAL CYS HIS HIS SER GLY ASN THR TYR PHE LEU SEQRES 6 A 177 ARG LYS GLN ALA ASN LEU LYS GLU MSE CYS LEU SER ALA SEQRES 7 A 177 LEU ALA ASN LEU THR TRP GLN SER ARG THR GLN ASP GLU SEQRES 8 A 177 HIS PRO LYS THR MSE PHE SER LYS ASP LYS ASP ILE ILE SEQRES 9 A 177 PRO PHE ILE ASP LYS TYR TRP GLU CYS MSE THR THR ARG SEQRES 10 A 177 GLN ARG PRO GLY LYS MSE THR TRP PRO ASN ASN ILE VAL SEQRES 11 A 177 LYS THR MSE SER LYS GLU ARG ASP VAL PHE LEU VAL LYS SEQRES 12 A 177 GLU HIS PRO ASP PRO GLY SER LYS ASP PRO GLU GLU ASP SEQRES 13 A 177 TYR PRO LYS PHE GLY LEU LEU ASP GLN ASP LEU SER ASN SEQRES 14 A 177 ILE GLY PRO ALA TYR ASP ASN GLN MODRES 3RSN MSE A 46 MET SELENOMETHIONINE MODRES 3RSN MSE A 74 MET SELENOMETHIONINE MODRES 3RSN MSE A 96 MET SELENOMETHIONINE MODRES 3RSN MSE A 114 MET SELENOMETHIONINE MODRES 3RSN MSE A 123 MET SELENOMETHIONINE MODRES 3RSN MSE A 133 MET SELENOMETHIONINE HET MSE A 46 8 HET MSE A 74 8 HET MSE A 96 8 HET MSE A 114 8 HET MSE A 123 8 HET MSE A 133 8 HET ZN A 200 1 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *75(H2 O) HELIX 1 1 ASP A 33 GLY A 36 5 4 HELIX 2 2 ASN A 70 ASP A 90 1 21 HELIX 3 3 ASP A 102 TYR A 110 1 9 HELIX 4 4 TRP A 111 MSE A 114 5 4 HELIX 5 5 THR A 124 ASN A 127 5 4 HELIX 6 6 ASN A 128 LYS A 135 1 8 HELIX 7 7 PRO A 153 TYR A 157 5 5 HELIX 8 8 ASP A 166 ILE A 170 5 5 SHEET 1 A 2 GLU A 20 GLN A 22 0 SHEET 2 A 2 TRP A 29 THR A 31 -1 O PHE A 30 N LEU A 21 SHEET 1 B 2 TYR A 49 HIS A 52 0 SHEET 2 B 2 TYR A 63 ARG A 66 -1 O LEU A 65 N SER A 50 SHEET 1 C 3 PHE A 97 SER A 98 0 SHEET 2 C 3 LYS A 159 LEU A 162 -1 O PHE A 160 N PHE A 97 SHEET 3 C 3 PHE A 140 LYS A 143 -1 N LEU A 141 O GLY A 161 LINK C PHE A 45 N MSE A 46 1555 1555 1.33 LINK C MSE A 46 N THR A 47 1555 1555 1.33 LINK C GLU A 73 N MSE A 74 1555 1555 1.32 LINK C MSE A 74 N CYS A 75 1555 1555 1.34 LINK C THR A 95 N MSE A 96 1555 1555 1.33 LINK C MSE A 96 N PHE A 97 1555 1555 1.33 LINK C CYS A 113 N MSE A 114 1555 1555 1.33 LINK C MSE A 114 N THR A 115 1555 1555 1.33 LINK C LYS A 122 N MSE A 123 1555 1555 1.33 LINK C MSE A 123 N THR A 124 1555 1555 1.32 LINK C THR A 132 N MSE A 133 1555 1555 1.32 LINK C MSE A 133 N SER A 134 1555 1555 1.33 LINK SG CYS A 56 ZN ZN A 200 1555 1555 2.26 LINK SG CYS A 26 ZN ZN A 200 1555 1555 2.41 LINK SG CYS A 53 ZN ZN A 200 1555 1555 2.48 LINK SG CYS A 23 ZN ZN A 200 1555 1555 2.52 CISPEP 1 TYR A 157 PRO A 158 0 5.76 SITE 1 AC1 4 CYS A 23 CYS A 26 CYS A 53 CYS A 56 CRYST1 49.984 49.984 165.519 90.00 90.00 120.00 P 31 2 1 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 0.020006 0.011551 0.000000 0.00000 SCALE2 0.000000 0.023101 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006042 0.00000