HEADER DNA BINDING PROTEIN 21-JUN-96 1SFE TITLE ADA O6-METHYLGUANINE-DNA METHYLTRANSFERASE FROM ESCHERICHIA COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADA O6-METHYLGUANINE-DNA METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL 19KD OF THE ADA PROTEIN; COMPND 5 EC: 2.1.1.63; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 37762; SOURCE 4 STRAIN: B; SOURCE 5 VARIANT: JM 101; SOURCE 6 GENE: ADAC; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PADAC; SOURCE 10 EXPRESSION_SYSTEM_GENE: ADAC; SOURCE 11 OTHER_DETAILS: TAC CONTROL KEYWDS ENZYME, TRANSFERASE, METHYLTRANSFERASE, NUCLEIC ACID BINDING PROTEIN, KEYWDS 2 DNA REPAIR PROTEIN, DNA-BINDING PROTEIN, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.H.MOORE,J.M.GULBIS,E.J.DODSON,B.DEMPLE,P.C.E.MOODY REVDAT 4 14-FEB-24 1SFE 1 KEYWDS REVDAT 3 13-JUL-11 1SFE 1 VERSN REVDAT 2 24-FEB-09 1SFE 1 VERSN REVDAT 1 23-DEC-96 1SFE 0 JRNL AUTH M.H.MOORE,J.M.GULBIS,E.J.DODSON,B.DEMPLE,P.C.MOODY JRNL TITL CRYSTAL STRUCTURE OF A SUICIDAL DNA REPAIR PROTEIN: THE ADA JRNL TITL 2 O6-METHYLGUANINE-DNA METHYLTRANSFERASE FROM E. COLI. JRNL REF EMBO J. V. 13 1495 1994 JRNL REFN ISSN 0261-4189 JRNL PMID 8156986 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.C.E.MOODY,M.H.MOORE REMARK 1 TITL CRYSTAL STRUCTURE OF E.COLI O6-METHYLGUANINE-DNA REMARK 1 TITL 2 METHYLTRANSFERASE REMARK 1 EDIT W.J.ZELLER, M.D'INCALCI, D.R.NEWELL REMARK 1 REF NOVEL APPROACHES IN 16 1995 REMARK 1 REF 2 ANTICANCER DRUG DESIGN : REMARK 1 REF 3 MOLECULAR MODELLING--NEW REMARK 1 REF 4 TREATMENT STRATEGIES (IN: REMARK 1 REF 5 CONTRIB.ONCOL., V.49) REMARK 1 PUBL BASEL : KARGER REMARK 1 REFN ISSN 3-8055-6043-5 REMARK 1 REFERENCE 2 REMARK 1 AUTH P.C.MOODY,B.DEMPLE REMARK 1 TITL CRYSTALLIZATION OF O6-METHYLGUANINE-DNA METHYLTRANSFERASE REMARK 1 TITL 2 FROM ESCHERICHIA COLI REMARK 1 REF J.MOL.BIOL. V. 200 751 1988 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 9017 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.2190 REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 9017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1257 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 145 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.90 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : 0.15 REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.010 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.031 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.033 ; 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) : 0.112 ; 0.150 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) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 3.900 ; 7.000 REMARK 3 STAGGERED (DEGREES) : 22.300; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 41.400; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.592 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.590 ; 3.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.597 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.580 ; 3.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1SFE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000176352. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL; NULL REMARK 200 TEMPERATURE (KELVIN) : NULL; NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; N REMARK 200 RADIATION SOURCE : PHOTON FACTORY; ROTATING ANODE REMARK 200 BEAMLINE : BL-6A; NULL REMARK 200 X-RAY GENERATOR MODEL : NULL; RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.89; 0.707 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : WEISSENBERG; RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9017 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.0 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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: NULL; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 22.97500 REMARK 290 SMTRY3 2 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 MET A 0 REMARK 465 THR A 1 REMARK 465 ALA A 2 REMARK 465 LYS A 3 REMARK 465 GLN A 4 REMARK 465 PHE A 5 REMARK 465 ARG A 6 REMARK 465 HIS A 7 REMARK 465 GLY A 8 REMARK 465 GLY A 9 REMARK 465 GLU A 10 REMARK 465 ASN A 11 REMARK 465 GLU A 177 REMARK 465 GLU A 178 REMARK 465 ARG A 179 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 ALA A 45 CB 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 25 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ASP A 59 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG A 92 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 105 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 129 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 165 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 165 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 171 CD - NE - CZ ANGL. DEV. = 16.4 DEGREES REMARK 500 ARG A 171 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 171 NE - CZ - NH2 ANGL. DEV. = -3.3 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 ASP A 64 98.96 -67.94 REMARK 500 ASP A 82 41.24 -145.33 REMARK 500 ALA A 127 40.27 -91.37 REMARK 500 ILE A 142 -50.41 69.17 REMARK 500 ALA A 174 72.83 -100.39 REMARK 500 REMARK 500 REMARK: NULL DBREF 1SFE A 0 179 UNP P06134 ADA_ECOLI 175 354 SEQRES 1 A 180 MET THR ALA LYS GLN PHE ARG HIS GLY GLY GLU ASN LEU SEQRES 2 A 180 ALA VAL ARG TYR ALA LEU ALA ASP CYS GLU LEU GLY ARG SEQRES 3 A 180 CYS LEU VAL ALA GLU SER GLU ARG GLY ILE CYS ALA ILE SEQRES 4 A 180 LEU LEU GLY ASP ASP ASP ALA THR LEU ILE SER GLU LEU SEQRES 5 A 180 GLN GLN MET PHE PRO ALA ALA ASP ASN ALA PRO ALA ASP SEQRES 6 A 180 LEU MET PHE GLN GLN HIS VAL ARG GLU VAL ILE ALA SER SEQRES 7 A 180 LEU ASN GLN ARG ASP THR PRO LEU THR LEU PRO LEU ASP SEQRES 8 A 180 ILE ARG GLY THR ALA PHE GLN GLN GLN VAL TRP GLN ALA SEQRES 9 A 180 LEU ARG THR ILE PRO CYS GLY GLU THR VAL SER TYR GLN SEQRES 10 A 180 GLN LEU ALA ASN ALA ILE GLY LYS PRO LYS ALA VAL ARG SEQRES 11 A 180 ALA VAL ALA SER ALA CYS ALA ALA ASN LYS LEU ALA ILE SEQRES 12 A 180 VAL ILE PRO CYS HIS ARG VAL VAL ARG GLY ASP GLY SER SEQRES 13 A 180 LEU SER GLY TYR ARG TRP GLY VAL SER ARG LYS ALA GLN SEQRES 14 A 180 LEU LEU ARG ARG GLU ALA GLU ASN GLU GLU ARG FORMUL 2 HOH *145(H2 O) HELIX 1 1 ASP A 44 MET A 54 1 11 HELIX 2 2 LEU A 65 ASN A 79 1 15 HELIX 3 3 ALA A 95 THR A 106 1 12 HELIX 4 4 TYR A 115 ALA A 121 1 7 HELIX 5 5 VAL A 128 ALA A 137 1 10 HELIX 6 6 CYS A 146 ARG A 148 5 3 HELIX 7 7 VAL A 163 GLU A 173 1 11 SHEET 1 A 3 ARG A 15 CYS A 21 0 SHEET 2 A 3 GLY A 24 GLU A 30 -1 N GLU A 30 O ARG A 15 SHEET 3 A 3 ILE A 35 GLY A 41 -1 N GLY A 41 O ARG A 25 CRYST1 46.200 45.950 46.400 90.00 114.06 90.00 P 1 21 1 2 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 0.021645 0.000000 0.009664 0.00000 SCALE2 0.000000 0.021763 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023602 0.00000