PDB Short entry for 1MGT HEADER TRANSFERASE 12-JAN-99 1MGT TITLE CRYSTAL STRUCTURE OF O6-METHYLGUANINE-DNA METHYLTRANSFERASE FROM TITLE 2 HYPERTHERMOPHILIC ARCHAEON PYROCOCCUS KODAKARAENSIS STRAIN KOD1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (O6-METHYLGUANINE-DNA METHYLTRANSFERASE); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MGMT; COMPND 5 EC: 2.1.1.63; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS; SOURCE 3 ORGANISM_TAXID: 69014; SOURCE 4 STRAIN: KOD1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS METHYLTRANSFERASE, DNA REPAIR PROTEIN, SUICIDAL ENZYME, KEYWDS 2 HYPERTHERMOSTABILITY, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.HASHIMOTO,T.INOUE,M.NISHIOKA,S.FUJIWARA,M.TAKAGI,T.IMANAKA,Y.KAI REVDAT 4 27-DEC-23 1MGT 1 REMARK REVDAT 3 13-JUL-11 1MGT 1 VERSN REVDAT 2 24-FEB-09 1MGT 1 VERSN REVDAT 1 07-JAN-00 1MGT 0 JRNL AUTH H.HASHIMOTO,T.INOUE,M.NISHIOKA,S.FUJIWARA,M.TAKAGI, JRNL AUTH 2 T.IMANAKA,Y.KAI JRNL TITL HYPERTHERMOSTABLE PROTEIN STRUCTURE MAINTAINED BY INTRA AND JRNL TITL 2 INTER-HELIX ION-PAIRS IN ARCHAEAL O6-METHYLGUANINE-DNA JRNL TITL 3 METHYLTRANSFERASE. JRNL REF J.MOL.BIOL. V. 292 707 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10497033 JRNL DOI 10.1006/JMBI.1999.3100 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.HASHIMOTO,M.NISHIOKA,T.INOUE,S.FUJIWARA,M.TAKAGI, REMARK 1 AUTH 2 T.IMANAKA,Y.KAI REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY CRYSTALLOGRAPHIC REMARK 1 TITL 2 ANALYSIS OF ARCHAEAL O6-METHYLGUANINE-DNA METHYLTRANSFERASE REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 54 1395 1998 REMARK 1 REFN ISSN 0907-4449 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 17597 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 825 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1333 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 129 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.23 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.013 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.023 ; 0.030 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.029 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : 15.000; NULL REMARK 3 PLANAR (DEGREES) : 1.700 ; 2.000 REMARK 3 STAGGERED (DEGREES) : 15.400; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 24.400; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.548 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.080 ; 3.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.400 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.751 ; 3.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1MGT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUL-99. REMARK 100 THE DEPOSITION ID IS D_1000007222. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-97 REMARK 200 TEMPERATURE (KELVIN) : 290 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-18B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : WEISSENBERG REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17669 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.16000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROP VAPOR DIFFUSION, PH 8.0 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 26.61500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 19.91500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.11000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 19.91500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.61500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.11000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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 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 LYS A 170 REMARK 465 GLU A 171 REMARK 465 TRP A 172 REMARK 465 THR A 173 REMARK 465 SER A 174 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (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,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 39 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 143 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES 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 SER A 21 77.83 -157.48 REMARK 500 ILE A 137 -66.16 77.07 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 SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 303 DBREF 1MGT A 1 174 UNP O74023 OGT_PYRKO 1 174 SEQRES 1 A 174 MET LEU SER VAL GLU LYS PHE ARG VAL GLY GLU ARG VAL SEQRES 2 A 174 VAL TRP ILE GLY VAL ILE PHE SER GLY ARG VAL GLN GLY SEQRES 3 A 174 ILE ALA PHE ALA PHE ASP ARG GLY THR LEU MET LYS ARG SEQRES 4 A 174 ILE HIS ASP LEU ALA GLU HIS LEU GLY LYS ARG GLY VAL SEQRES 5 A 174 SER ILE SER LEU ASP VAL GLN PRO SER ASP TYR PRO GLU SEQRES 6 A 174 LYS VAL PHE LYS VAL LEU ILE GLY GLU LEU ASP ASN ALA SEQRES 7 A 174 SER PHE LEU ARG GLU LEU SER PHE GLU GLY VAL THR PRO SEQRES 8 A 174 PHE GLU LYS LYS VAL TYR GLU TRP LEU THR LYS ASN VAL SEQRES 9 A 174 LYS ARG GLY SER VAL ILE THR TYR GLY ASP LEU ALA LYS SEQRES 10 A 174 ALA LEU ASN THR SER PRO ARG ALA VAL GLY GLY ALA MET SEQRES 11 A 174 LYS ARG ASN PRO TYR PRO ILE VAL VAL PRO CYS HIS ARG SEQRES 12 A 174 VAL VAL ALA HIS ASP GLY ILE GLY TYR TYR SER SER GLY SEQRES 13 A 174 ILE GLU GLU LYS LYS PHE LEU LEU GLU ILE GLU GLY VAL SEQRES 14 A 174 LYS GLU TRP THR SER HET SO4 A 301 5 HET SO4 A 302 5 HET SO4 A 303 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 HOH *129(H2 O) HELIX 1 1 ARG A 33 ARG A 50 1 18 HELIX 2 2 TYR A 63 LEU A 71 1 9 HELIX 3 3 ASN A 77 GLU A 83 5 7 HELIX 4 4 PRO A 91 ASN A 103 1 13 HELIX 5 5 TYR A 112 ALA A 118 1 7 HELIX 6 6 PRO A 123 LYS A 131 1 9 HELIX 7 7 CYS A 141 ARG A 143 5 3 HELIX 8 8 ILE A 157 ILE A 166 1 10 SHEET 1 A 3 LEU A 2 VAL A 9 0 SHEET 2 A 3 ARG A 12 SER A 21 -1 N VAL A 18 O SER A 3 SHEET 3 A 3 ARG A 23 ALA A 30 -1 N ALA A 30 O TRP A 15 SITE 1 AC1 9 ARG A 8 THR A 111 TYR A 112 GLY A 113 SITE 2 AC1 9 ALA A 146 HIS A 147 HOH A 539 HOH A 540 SITE 3 AC1 9 HOH A 600 SITE 1 AC2 5 LYS A 6 ARG A 8 ARG A 124 HOH A 547 SITE 2 AC2 5 HOH A 621 SITE 1 AC3 4 HIS A 46 ARG A 50 ASN A 120 ARG A 132 CRYST1 53.230 86.220 39.830 90.00 90.00 90.00 P 21 21 21 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 0.018786 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011598 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025107 0.00000