HEADER TRANSFERASE 21-MAY-15 4ZYG TITLE CRYSTAL STRUCTURE OF METHYLATED SULFOLOBUS SOLFATARICUS O6- TITLE 2 METHYLGUANINE METHYLTRANSFERASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYLATED-DNA--PROTEIN-CYSTEINE METHYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 6-O-METHYLGUANINE-DNA METHYLTRANSFERASE,MGMT,O-6- COMPND 5 METHYLGUANINE-DNA-ALKYLTRANSFERASE; COMPND 6 EC: 2.1.1.63; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS; SOURCE 3 ORGANISM_TAXID: 2287; SOURCE 4 STRAIN: ATCC 35092 / DSM 1617 / JCM 11322 / P2; SOURCE 5 GENE: OGT, SSO2487; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PQE31 KEYWDS EXTREMOPHILES, DNA REPAIR, ALKYLATED DNA-PROTEIN ALKYLTRANSFERASE, KEYWDS 2 METHYLATED PROTEIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.MIGGIANO,F.ROSSI,M.RIZZI REVDAT 3 10-JAN-24 4ZYG 1 REMARK REVDAT 2 28-OCT-15 4ZYG 1 JRNL REVDAT 1 12-AUG-15 4ZYG 0 JRNL AUTH G.PERUGINO,R.MIGGIANO,M.SERPE,A.VETTONE,A.VALENTI,S.LAHIRI, JRNL AUTH 2 F.ROSSI,M.ROSSI,M.RIZZI,M.CIARAMELLA JRNL TITL STRUCTURE-FUNCTION RELATIONSHIPS GOVERNING ACTIVITY AND JRNL TITL 2 STABILITY OF A DNA ALKYLATION DAMAGE REPAIR THERMOSTABLE JRNL TITL 3 PROTEIN. JRNL REF NUCLEIC ACIDS RES. V. 43 8801 2015 JRNL REFN ESSN 1362-4962 JRNL PMID 26227971 JRNL DOI 10.1093/NAR/GKV774 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1690 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 8729 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.740 REMARK 3 FREE R VALUE TEST SET COUNT : 414 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 47.3565 - 4.0380 0.94 2811 143 0.1691 0.2383 REMARK 3 2 4.0380 - 3.2053 0.97 2764 130 0.1866 0.3157 REMARK 3 3 3.2053 - 2.8002 0.98 2740 141 0.2416 0.3429 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.100 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 : 0.009 2443 REMARK 3 ANGLE : 1.194 3287 REMARK 3 CHIRALITY : 0.049 363 REMARK 3 PLANARITY : 0.007 411 REMARK 3 DIHEDRAL : 14.866 928 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 4ZYG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-MAY-15. REMARK 100 THE DEPOSITION ID IS D_1000210118. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.972 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8764 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 47.350 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.12900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.48100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1WRJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM ACETATE 0.1 M, BIS-TRIS 0.1 M REMARK 280 PH 5.5, 17% PEG 17000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277.15K 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 24.24300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 71.01300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.11150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 71.01300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.24300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.11150 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: 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 350 REMARK 350 BIOMOLECULE: 2 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: B 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 PRO B 150 REMARK 465 GLU B 151 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 ALA A 17 114.79 -164.76 REMARK 500 ASP A 19 -156.66 -114.82 REMARK 500 CYS A 29 170.41 178.49 REMARK 500 ARG A 61 114.80 -172.12 REMARK 500 LEU A 115 -59.89 58.58 REMARK 500 TYR A 131 142.65 -179.06 REMARK 500 PRO A 150 -164.65 -73.72 REMARK 500 ASP B 19 -160.98 -113.74 REMARK 500 CYS B 29 -178.59 179.18 REMARK 500 MET B 80 1.82 -69.64 REMARK 500 THR B 99 -153.30 -148.94 REMARK 500 LEU B 115 -59.96 64.92 REMARK 500 TYR B 131 117.68 -163.17 REMARK 500 REMARK 500 REMARK: NULL DBREF 4ZYG A 1 151 UNP Q97VW7 OGT_SULSO 1 151 DBREF 4ZYG B 1 151 UNP Q97VW7 OGT_SULSO 1 151 SEQRES 1 A 151 MET LEU VAL TYR GLY LEU TYR LYS SER PRO LEU GLY TYR SEQRES 2 A 151 ILE THR VAL ALA LYS ASP ASP LYS GLY PHE ILE MET LEU SEQRES 3 A 151 ASP PHE CYS ASP CYS VAL GLU GLY ASN SER ARG ASP ASP SEQRES 4 A 151 SER SER PHE THR GLU PHE PHE HIS LYS LEU ASP LEU TYR SEQRES 5 A 151 PHE GLU GLY LYS PRO ILE ASN LEU ARG GLU PRO ILE ASN SEQRES 6 A 151 LEU LYS THR TYR PRO PHE ARG LEU SER VAL PHE LYS GLU SEQRES 7 A 151 VAL MET LYS ILE PRO TRP GLY LYS VAL MET THR TYR LYS SEQRES 8 A 151 GLN ILE ALA ASP SER LEU GLY THR SER PRO ARG ALA VAL SEQRES 9 A 151 GLY MET ALA LEU SER LYS ASN PRO ILE LEU LEU ILE ILE SEQRES 10 A 151 PRO SMC HIS ARG VAL ILE ALA GLU ASN GLY ILE GLY GLY SEQRES 11 A 151 TYR SER ARG GLY VAL LYS LEU LYS ARG ALA LEU LEU GLU SEQRES 12 A 151 LEU GLU GLY VAL LYS ILE PRO GLU SEQRES 1 B 151 MET LEU VAL TYR GLY LEU TYR LYS SER PRO LEU GLY TYR SEQRES 2 B 151 ILE THR VAL ALA LYS ASP ASP LYS GLY PHE ILE MET LEU SEQRES 3 B 151 ASP PHE CYS ASP CYS VAL GLU GLY ASN SER ARG ASP ASP SEQRES 4 B 151 SER SER PHE THR GLU PHE PHE HIS LYS LEU ASP LEU TYR SEQRES 5 B 151 PHE GLU GLY LYS PRO ILE ASN LEU ARG GLU PRO ILE ASN SEQRES 6 B 151 LEU LYS THR TYR PRO PHE ARG LEU SER VAL PHE LYS GLU SEQRES 7 B 151 VAL MET LYS ILE PRO TRP GLY LYS VAL MET THR TYR LYS SEQRES 8 B 151 GLN ILE ALA ASP SER LEU GLY THR SER PRO ARG ALA VAL SEQRES 9 B 151 GLY MET ALA LEU SER LYS ASN PRO ILE LEU LEU ILE ILE SEQRES 10 B 151 PRO SMC HIS ARG VAL ILE ALA GLU ASN GLY ILE GLY GLY SEQRES 11 B 151 TYR SER ARG GLY VAL LYS LEU LYS ARG ALA LEU LEU GLU SEQRES 12 B 151 LEU GLU GLY VAL LYS ILE PRO GLU MODRES 4ZYG SMC A 119 CYS MODIFIED RESIDUE MODRES 4ZYG SMC B 119 CYS MODIFIED RESIDUE HET SMC A 119 7 HET SMC B 119 7 HETNAM SMC S-METHYLCYSTEINE FORMUL 1 SMC 2(C4 H9 N O2 S) FORMUL 3 HOH *12(H2 O) HELIX 1 AA1 ASP A 38 SER A 41 5 4 HELIX 2 AA2 PHE A 42 GLU A 54 1 13 HELIX 3 AA3 TYR A 69 MET A 80 1 12 HELIX 4 AA4 TYR A 90 GLY A 98 1 9 HELIX 5 AA5 SER A 100 SER A 109 1 10 HELIX 6 AA6 PRO A 118 HIS A 120 5 3 HELIX 7 AA7 GLY A 134 GLU A 145 1 12 HELIX 8 AA8 ASP B 38 SER B 41 5 4 HELIX 9 AA9 PHE B 42 GLU B 54 1 13 HELIX 10 AB1 TYR B 69 MET B 80 1 12 HELIX 11 AB2 TYR B 90 ASP B 95 1 6 HELIX 12 AB3 SER B 100 SER B 109 1 10 HELIX 13 AB4 PRO B 118 HIS B 120 5 3 HELIX 14 AB5 GLY B 134 GLU B 145 1 12 SHEET 1 AA1 3 VAL A 3 SER A 9 0 SHEET 2 AA1 3 GLY A 12 LYS A 18 -1 O ILE A 14 N TYR A 7 SHEET 3 AA1 3 PHE A 23 ASP A 27 -1 O ILE A 24 N ALA A 17 SHEET 1 AA2 2 MET A 88 THR A 89 0 SHEET 2 AA2 2 VAL A 122 ILE A 123 1 O ILE A 123 N MET A 88 SHEET 1 AA3 3 VAL B 3 SER B 9 0 SHEET 2 AA3 3 GLY B 12 LYS B 18 -1 O ILE B 14 N TYR B 7 SHEET 3 AA3 3 PHE B 23 PHE B 28 -1 O ILE B 24 N ALA B 17 SHEET 1 AA4 2 MET B 88 THR B 89 0 SHEET 2 AA4 2 VAL B 122 ILE B 123 1 O ILE B 123 N MET B 88 SSBOND 1 CYS A 29 CYS A 31 1555 1555 2.04 SSBOND 2 CYS B 29 CYS B 31 1555 1555 2.03 LINK C PRO A 118 N SMC A 119 1555 1555 1.33 LINK C SMC A 119 N HIS A 120 1555 1555 1.33 LINK C PRO B 118 N SMC B 119 1555 1555 1.33 LINK C SMC B 119 N HIS B 120 1555 1555 1.32 CISPEP 1 MET A 1 LEU A 2 0 3.20 CRYST1 48.486 50.223 142.026 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 0.020625 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019911 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007041 0.00000