HEADER TRANSFERASE 02-APR-13 4BHB TITLE CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS O6- TITLE 2 METHYLGUANINE METHYLTRANSFERASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYLATED-DNA--PROTEIN-CYSTEINE METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 6-O-METHYLGUANINE-DNA METHYLTRANSFERASE, MGMT, COMPND 5 O-6-METHYLGUANINE-DNA-ALKYLTRANSFERASE; COMPND 6 EC: 2.1.1.63; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET16B KEYWDS TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.MIGGIANO,V.CASAZZA,S.GARAVAGLIA,M.CIARAMELLA,G.PERUGINO,M.RIZZII, AUTHOR 2 F.ROSSI REVDAT 2 12-JUN-13 4BHB 1 JRNL REVDAT 1 17-APR-13 4BHB 0 JRNL AUTH R.MIGGIANO,V.CASAZZA,S.GARAVAGLIA,M.CIARAMELLA,G.PERUGINO, JRNL AUTH 2 M.RIZZI,F.ROSSI JRNL TITL BIOCHEMICAL AND STRUCTURAL STUDIES OF THE MYCOBACTERIUM JRNL TITL 2 TUBERCULOSIS O6-METHYLGUANINE METHYLTRANSFERASE AND MUTATED JRNL TITL 3 VARIANTS. JRNL REF J.BACTERIOL. V. 195 2728 2013 JRNL REFN ISSN 0021-9193 JRNL PMID 23564173 JRNL DOI 10.1128/JB.02298-12 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT 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) : 1.800 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.896 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.35 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.29 REMARK 3 NUMBER OF REFLECTIONS : 17648 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.2280 REMARK 3 R VALUE (WORKING SET) : 0.2268 REMARK 3 FREE R VALUE : 0.2938 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.0 REMARK 3 FREE R VALUE TEST SET COUNT : 362 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 27.8995 - 2.5957 0.98 5864 111 0.2033 0.2786 REMARK 3 2 2.5957 - 2.0605 1.00 5724 143 0.2794 0.3065 REMARK 3 3 2.0605 - 1.8001 1.00 5698 108 0.2720 0.3543 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) : 0.26 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.66 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.39 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.3 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 1300 REMARK 3 ANGLE : 1.119 1765 REMARK 3 CHIRALITY : 0.073 195 REMARK 3 PLANARITY : 0.005 231 REMARK 3 DIHEDRAL : 14.088 472 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 4BHB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-APR-13. REMARK 100 THE PDBE ID CODE IS EBI-56364. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL 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 : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17690 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.80 REMARK 200 RESOLUTION RANGE LOW (A) : 40.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.0 REMARK 200 R MERGE (I) : 0.05 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.80 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 FOR SHELL : NULL 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: PDB ENTRY 1SFE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.5 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 29.56700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.87600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.56700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.87600 REMARK 290 SMTRY3 4 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 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 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 OD2 ASP A 165 O HOH A 2116 2.17 REMARK 500 O HOH A 2024 O HOH A 2025 2.04 REMARK 500 O HOH A 2024 O HOH A 2028 2.12 REMARK 500 O HOH A 2026 O HOH A 2031 2.08 REMARK 500 O HOH A 2071 O HOH A 2077 1.88 REMARK 500 O HOH A 2095 O HOH A 2096 2.07 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 2025 O HOH A 2069 4456 1.96 REMARK 500 O HOH A 2025 O HOH A 2096 4456 2.15 REMARK 500 O HOH A 2053 O HOH A 2058 2665 1.95 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 43 83.21 -153.21 REMARK 500 PRO A 44 0.45 -57.87 REMARK 500 ILE A 122 -63.73 64.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1166 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1167 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4BHC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE M. TUBERCULOSIS O6- REMARK 900 METHYLGUANINE METHYLTRANSFERASE R37L VARIANT REMARK 999 REMARK 999 SEQUENCE REMARK 999 ILE 2 HAS BEEN REPLACED BY VAL DBREF 4BHB A 1 165 UNP P0A696 OGT_MYCTU 1 165 SEQADV 4BHB VAL A 2 UNP P0A696 ILE 2 ENGINEERED MUTATION SEQRES 1 A 165 MET VAL HIS TYR ARG THR ILE ASP SER PRO ILE GLY PRO SEQRES 2 A 165 LEU THR LEU ALA GLY HIS GLY SER VAL LEU THR ASN LEU SEQRES 3 A 165 ARG MET LEU GLU GLN THR TYR GLU PRO SER ARG THR HIS SEQRES 4 A 165 TRP THR PRO ASP PRO GLY ALA PHE SER GLY ALA VAL ASP SEQRES 5 A 165 GLN LEU ASN ALA TYR PHE ALA GLY GLU LEU THR GLU PHE SEQRES 6 A 165 ASP VAL GLU LEU ASP LEU ARG GLY THR ASP PHE GLN GLN SEQRES 7 A 165 ARG VAL TRP LYS ALA LEU LEU THR ILE PRO TYR GLY GLU SEQRES 8 A 165 THR ARG SER TYR GLY GLU ILE ALA ASP GLN ILE GLY ALA SEQRES 9 A 165 PRO GLY ALA ALA ARG ALA VAL GLY LEU ALA ASN GLY HIS SEQRES 10 A 165 ASN PRO ILE ALA ILE ILE VAL PRO CYS HIS ARG VAL ILE SEQRES 11 A 165 GLY ALA SER GLY LYS LEU THR GLY TYR GLY GLY GLY ILE SEQRES 12 A 165 ASN ARG LYS ARG ALA LEU LEU GLU LEU GLU LYS SER ARG SEQRES 13 A 165 ALA PRO ALA ASP LEU THR LEU PHE ASP HET GOL A1166 6 HET GOL A1167 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 2(C3 H8 O3) FORMUL 3 HOH *118(H2 O) HELIX 1 1 GLU A 34 TRP A 40 5 7 HELIX 2 2 PHE A 47 ALA A 59 1 13 HELIX 3 3 THR A 74 LEU A 85 1 12 HELIX 4 4 SER A 94 ILE A 102 1 9 HELIX 5 5 ALA A 107 HIS A 117 1 11 HELIX 6 6 PRO A 125 ARG A 128 5 4 HELIX 7 7 GLY A 141 SER A 155 1 15 HELIX 8 8 ASP A 160 ASP A 165 5 6 SHEET 1 AA 4 VAL A 22 ARG A 27 0 SHEET 2 AA 4 LEU A 14 HIS A 19 -1 O THR A 15 N ARG A 27 SHEET 3 AA 4 HIS A 3 ILE A 7 -1 O HIS A 3 N GLY A 18 SHEET 4 AA 4 THR A 41 PRO A 42 1 O THR A 41 N TYR A 4 SITE 1 AC1 4 MET A 28 ARG A 145 HOH A2011 HOH A2107 SITE 1 AC2 7 HIS A 39 PHE A 65 VAL A 67 LEU A 69 SITE 2 AC2 7 LEU A 85 ILE A 123 HOH A2047 CRYST1 59.134 81.752 38.165 90.00 90.00 90.00 P 21 21 2 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 0.016911 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012232 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026202 0.00000 MASTER 262 0 2 8 4 0 3 6 0 0 0 13 END