HEADER HYDROLASE, LYASE/DNA 12-NOV-09 3KNT TITLE CRYSTAL STRUCTURE OF METHANOCALDOCOCCUS JANNASCHII 8-OXOGUANINE TITLE 2 GLYCOSYLASE/LYASE IN COMPLEX WITH 15MER DNA CONTAINING 8-OXOGUANINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-GLYCOSYLASE/DNA LYASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: MJAOGG; COMPND 5 SYNONYM: 8-OXOGUANINE DNA GLYCOSYLASE, DNA-(APURINIC OR APYRIMIDINIC COMPND 6 SITE) LYASE, AP LYASE; COMPND 7 EC: 3.2.2.-, 4.2.99.18; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: 5'-D(*AP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3'; COMPND 12 CHAIN: E, G, I, K; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: 5'-D(*TP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3'; COMPND 16 CHAIN: F, H, J, L; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_COMMON: METHANOCOCCUS JANNASCHII; SOURCE 4 ORGANISM_TAXID: 2190; SOURCE 5 GENE: 1451601, MJ0724, OGG; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ER2566(FPG-); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-22; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN HUMANS.; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN HUMANS. KEYWDS PROTEIN-DNA COMPLEX, OGG, HELIX-HAIRPIN-HELIX, GLYCOSYLASE, 8- KEYWDS 2 OXOGUANINE, 8-OXOG, DNA REPAIR, DNA DAMAGE, GLYCOSIDASE, KEYWDS 3 MULTIFUNCTIONAL ENZYME, NUCLEASE, HYDROLASE, LYASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR F.FAUCHER,S.DOUBLIE REVDAT 5 06-SEP-23 3KNT 1 REMARK REVDAT 4 13-OCT-21 3KNT 1 REMARK SEQADV LINK REVDAT 3 01-NOV-17 3KNT 1 REMARK REVDAT 2 16-MAR-10 3KNT 1 JRNL REVDAT 1 02-FEB-10 3KNT 0 JRNL AUTH F.FAUCHER,S.S.WALLACE,S.DOUBLIE JRNL TITL THE C-TERMINAL LYSINE OF OGG2 DNA GLYCOSYLASES IS A MAJOR JRNL TITL 2 MOLECULAR DETERMINANT FOR GUANINE/8-OXOGUANINE DISTINCTION. JRNL REF J.MOL.BIOL. V. 397 46 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20083120 JRNL DOI 10.1016/J.JMB.2010.01.024 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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 : TWIN_LSQ_F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 37810 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1899 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 19.8404 - 7.0989 0.98 1928 99 0.1502 0.1915 REMARK 3 2 7.0989 - 5.6781 0.98 1896 103 0.1916 0.2604 REMARK 3 3 5.6781 - 4.9733 0.98 1900 96 0.1669 0.2338 REMARK 3 4 4.9733 - 4.5245 0.98 1896 92 0.1518 0.1605 REMARK 3 5 4.5245 - 4.2035 0.98 1897 108 0.1510 0.1889 REMARK 3 6 4.2035 - 3.9577 0.98 1881 86 0.1671 0.1807 REMARK 3 7 3.9577 - 3.7609 0.98 1902 98 0.1763 0.2003 REMARK 3 8 3.7609 - 3.5982 0.98 1865 112 0.1792 0.2012 REMARK 3 9 3.5982 - 3.4604 0.98 1893 100 0.1929 0.2243 REMARK 3 10 3.4604 - 3.3416 0.98 1889 114 0.2091 0.2250 REMARK 3 11 3.3416 - 3.2376 0.98 1865 93 0.2231 0.2529 REMARK 3 12 3.2376 - 3.1454 0.98 1924 97 0.2318 0.2529 REMARK 3 13 3.1454 - 3.0629 0.98 1883 100 0.2318 0.2669 REMARK 3 14 3.0629 - 2.9884 0.98 1870 104 0.2603 0.3021 REMARK 3 15 2.9884 - 2.9207 0.98 1900 91 0.2673 0.3370 REMARK 3 16 2.9207 - 2.8587 0.98 1859 126 0.2830 0.3022 REMARK 3 17 2.8587 - 2.8017 0.98 1916 92 0.2996 0.3530 REMARK 3 18 2.8017 - 2.7490 0.98 1843 101 0.3094 0.3522 REMARK 3 19 2.7490 - 2.7000 0.98 1910 81 0.3075 0.3441 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 : 0.31 REMARK 3 B_SOL : 59.08 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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 : 0.004 9675 REMARK 3 ANGLE : 0.984 13464 REMARK 3 CHIRALITY : 0.068 1469 REMARK 3 PLANARITY : 0.002 1326 REMARK 3 DIHEDRAL : 22.615 3870 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 3KNT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-NOV-09. REMARK 100 THE DEPOSITION ID IS D_1000056223. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL CRYO-COOLED REMARK 200 SI(111) REMARK 200 OPTICS : ADJUSTABLE FOCUS K-B PAIR SI REMARK 200 PLUS PT, RH COATINGS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37810 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 19.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.820 REMARK 200 R MERGE (I) : 0.12400 REMARK 200 R SYM (I) : 0.07100 REMARK 200 FOR THE DATA SET : 12.5800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.87 REMARK 200 R MERGE FOR SHELL (I) : 0.01044 REMARK 200 R SYM FOR SHELL (I) : 0.81700 REMARK 200 FOR SHELL : 1.720 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 3FHF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG-8000 16%, 0.1M NACL, PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 75.01500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5 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: DODECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, J, REMARK 350 AND CHAINS: K, L 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, E, F 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: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, G, H 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: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, I, J 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: 5 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, K, L 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 C 1 REMARK 465 MET C 2 REMARK 465 MET D 1 REMARK 465 DC G 29 REMARK 465 DC G 30 REMARK 465 DT H 1 REMARK 465 DG H 2 REMARK 465 DC I 30 REMARK 465 DT J 1 REMARK 465 DG J 2 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 DG H 3 P OP1 OP2 REMARK 470 DG J 3 P OP1 OP2 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 O ALA B 144 OH TYR B 172 2.15 REMARK 500 REMARK 500 REMARK: NULL 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 DC E 21 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 8OG E 23 O3' - P - O5' ANGL. DEV. = -12.1 DEGREES REMARK 500 DC F 8 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 8OG G 23 O3' - P - O5' ANGL. DEV. = -13.2 DEGREES REMARK 500 DG H 11 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DA H 13 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT I 19 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA I 22 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 8OG I 23 O3' - P - O5' ANGL. DEV. = -12.1 DEGREES REMARK 500 8OG K 23 O3' - P - O5' ANGL. DEV. = -12.7 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 25.87 -78.07 REMARK 500 LEU A 81 3.40 -69.36 REMARK 500 LYS A 100 -9.98 -58.89 REMARK 500 ASN A 101 55.27 -101.57 REMARK 500 ASN A 111 -147.39 -134.22 REMARK 500 GLU A 130 2.17 -67.52 REMARK 500 ASP A 142 35.53 -76.16 REMARK 500 ASN A 187 72.47 66.12 REMARK 500 LEU A 206 -105.71 -95.10 REMARK 500 ASN B 12 41.31 -100.92 REMARK 500 ASP B 64 5.14 -65.75 REMARK 500 LEU B 69 123.86 -34.71 REMARK 500 PHE B 85 73.99 -107.16 REMARK 500 ASN B 101 67.60 -103.49 REMARK 500 ASP B 142 58.86 -104.72 REMARK 500 ILE B 146 73.71 -100.16 REMARK 500 ARG B 201 -62.08 -95.10 REMARK 500 VAL B 205 74.73 -107.55 REMARK 500 LEU B 206 -92.00 -88.85 REMARK 500 PHE C 99 42.99 -106.55 REMARK 500 ASN C 111 -165.26 -128.68 REMARK 500 LEU C 206 -93.29 -108.68 REMARK 500 GLU D 14 12.62 -67.65 REMARK 500 PHE D 99 51.16 -112.11 REMARK 500 ASN D 137 -6.27 -59.62 REMARK 500 VAL D 205 38.92 -93.96 REMARK 500 LEU D 206 -102.32 -51.27 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 NA A 208 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 120 O REMARK 620 2 ILE A 123 O 106.8 REMARK 620 3 ILE A 126 O 88.6 95.3 REMARK 620 4 DC E 26 OP1 156.3 88.7 108.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 208 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL B 120 O REMARK 620 2 ILE B 123 O 120.0 REMARK 620 3 ILE B 126 O 81.3 89.7 REMARK 620 4 DC G 26 OP1 141.9 98.0 97.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA C 208 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL C 120 O REMARK 620 2 ILE C 123 O 96.0 REMARK 620 3 ILE C 126 O 84.3 89.2 REMARK 620 4 DC I 26 OP1 173.9 87.1 101.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA D 208 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL D 120 O REMARK 620 2 ILE D 123 O 93.1 REMARK 620 3 ILE D 126 O 91.0 98.3 REMARK 620 4 DC K 26 OP1 172.4 87.7 96.3 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 NA A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA C 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA D 208 DBREF 3KNT A 1 207 UNP Q58134 OGG1_METJA 1 207 DBREF 3KNT B 1 207 UNP Q58134 OGG1_METJA 1 207 DBREF 3KNT C 1 207 UNP Q58134 OGG1_METJA 1 207 DBREF 3KNT D 1 207 UNP Q58134 OGG1_METJA 1 207 DBREF 3KNT E 16 30 PDB 3KNT 3KNT 16 30 DBREF 3KNT G 16 30 PDB 3KNT 3KNT 16 30 DBREF 3KNT I 16 30 PDB 3KNT 3KNT 16 30 DBREF 3KNT K 16 30 PDB 3KNT 3KNT 16 30 DBREF 3KNT F 1 15 PDB 3KNT 3KNT 1 15 DBREF 3KNT H 1 15 PDB 3KNT 3KNT 1 15 DBREF 3KNT J 1 15 PDB 3KNT 3KNT 1 15 DBREF 3KNT L 1 15 PDB 3KNT 3KNT 1 15 SEQADV 3KNT GLN A 129 UNP Q58134 LYS 129 ENGINEERED MUTATION SEQADV 3KNT GLN B 129 UNP Q58134 LYS 129 ENGINEERED MUTATION SEQADV 3KNT GLN C 129 UNP Q58134 LYS 129 ENGINEERED MUTATION SEQADV 3KNT GLN D 129 UNP Q58134 LYS 129 ENGINEERED MUTATION SEQRES 1 A 207 MET MET LEU ILE LYS LYS ILE GLU GLU LEU LYS ASN SER SEQRES 2 A 207 GLU ILE LYS ASP ILE ILE ASP LYS ARG ILE GLN GLU PHE SEQRES 3 A 207 LYS SER PHE LYS ASN LYS SER ASN GLU GLU TRP PHE LYS SEQRES 4 A 207 GLU LEU CYS PHE CYS ILE LEU THR ALA ASN PHE THR ALA SEQRES 5 A 207 GLU GLY GLY ILE ARG ILE GLN LYS GLU ILE GLY ASP GLY SEQRES 6 A 207 PHE LEU THR LEU PRO ARG GLU GLU LEU GLU GLU LYS LEU SEQRES 7 A 207 LYS ASN LEU GLY HIS ARG PHE TYR ARG LYS ARG ALA GLU SEQRES 8 A 207 TYR ILE VAL LEU ALA ARG ARG PHE LYS ASN ILE LYS ASP SEQRES 9 A 207 ILE VAL GLU SER PHE GLU ASN GLU LYS VAL ALA ARG GLU SEQRES 10 A 207 PHE LEU VAL ARG ASN ILE LYS GLY ILE GLY TYR GLN GLU SEQRES 11 A 207 ALA SER HIS PHE LEU ARG ASN VAL GLY TYR ASP ASP VAL SEQRES 12 A 207 ALA ILE ILE ASP ARG HIS ILE LEU ARG GLU LEU TYR GLU SEQRES 13 A 207 ASN ASN TYR ILE ASP GLU ILE PRO LYS THR LEU SER ARG SEQRES 14 A 207 ARG LYS TYR LEU GLU ILE GLU ASN ILE LEU ARG ASP ILE SEQRES 15 A 207 GLY GLU GLU VAL ASN LEU LYS LEU SER GLU LEU ASP LEU SEQRES 16 A 207 TYR ILE TRP TYR LEU ARG THR GLY LYS VAL LEU LYS SEQRES 1 B 207 MET MET LEU ILE LYS LYS ILE GLU GLU LEU LYS ASN SER SEQRES 2 B 207 GLU ILE LYS ASP ILE ILE ASP LYS ARG ILE GLN GLU PHE SEQRES 3 B 207 LYS SER PHE LYS ASN LYS SER ASN GLU GLU TRP PHE LYS SEQRES 4 B 207 GLU LEU CYS PHE CYS ILE LEU THR ALA ASN PHE THR ALA SEQRES 5 B 207 GLU GLY GLY ILE ARG ILE GLN LYS GLU ILE GLY ASP GLY SEQRES 6 B 207 PHE LEU THR LEU PRO ARG GLU GLU LEU GLU GLU LYS LEU SEQRES 7 B 207 LYS ASN LEU GLY HIS ARG PHE TYR ARG LYS ARG ALA GLU SEQRES 8 B 207 TYR ILE VAL LEU ALA ARG ARG PHE LYS ASN ILE LYS ASP SEQRES 9 B 207 ILE VAL GLU SER PHE GLU ASN GLU LYS VAL ALA ARG GLU SEQRES 10 B 207 PHE LEU VAL ARG ASN ILE LYS GLY ILE GLY TYR GLN GLU SEQRES 11 B 207 ALA SER HIS PHE LEU ARG ASN VAL GLY TYR ASP ASP VAL SEQRES 12 B 207 ALA ILE ILE ASP ARG HIS ILE LEU ARG GLU LEU TYR GLU SEQRES 13 B 207 ASN ASN TYR ILE ASP GLU ILE PRO LYS THR LEU SER ARG SEQRES 14 B 207 ARG LYS TYR LEU GLU ILE GLU ASN ILE LEU ARG ASP ILE SEQRES 15 B 207 GLY GLU GLU VAL ASN LEU LYS LEU SER GLU LEU ASP LEU SEQRES 16 B 207 TYR ILE TRP TYR LEU ARG THR GLY LYS VAL LEU LYS SEQRES 1 C 207 MET MET LEU ILE LYS LYS ILE GLU GLU LEU LYS ASN SER SEQRES 2 C 207 GLU ILE LYS ASP ILE ILE ASP LYS ARG ILE GLN GLU PHE SEQRES 3 C 207 LYS SER PHE LYS ASN LYS SER ASN GLU GLU TRP PHE LYS SEQRES 4 C 207 GLU LEU CYS PHE CYS ILE LEU THR ALA ASN PHE THR ALA SEQRES 5 C 207 GLU GLY GLY ILE ARG ILE GLN LYS GLU ILE GLY ASP GLY SEQRES 6 C 207 PHE LEU THR LEU PRO ARG GLU GLU LEU GLU GLU LYS LEU SEQRES 7 C 207 LYS ASN LEU GLY HIS ARG PHE TYR ARG LYS ARG ALA GLU SEQRES 8 C 207 TYR ILE VAL LEU ALA ARG ARG PHE LYS ASN ILE LYS ASP SEQRES 9 C 207 ILE VAL GLU SER PHE GLU ASN GLU LYS VAL ALA ARG GLU SEQRES 10 C 207 PHE LEU VAL ARG ASN ILE LYS GLY ILE GLY TYR GLN GLU SEQRES 11 C 207 ALA SER HIS PHE LEU ARG ASN VAL GLY TYR ASP ASP VAL SEQRES 12 C 207 ALA ILE ILE ASP ARG HIS ILE LEU ARG GLU LEU TYR GLU SEQRES 13 C 207 ASN ASN TYR ILE ASP GLU ILE PRO LYS THR LEU SER ARG SEQRES 14 C 207 ARG LYS TYR LEU GLU ILE GLU ASN ILE LEU ARG ASP ILE SEQRES 15 C 207 GLY GLU GLU VAL ASN LEU LYS LEU SER GLU LEU ASP LEU SEQRES 16 C 207 TYR ILE TRP TYR LEU ARG THR GLY LYS VAL LEU LYS SEQRES 1 D 207 MET MET LEU ILE LYS LYS ILE GLU GLU LEU LYS ASN SER SEQRES 2 D 207 GLU ILE LYS ASP ILE ILE ASP LYS ARG ILE GLN GLU PHE SEQRES 3 D 207 LYS SER PHE LYS ASN LYS SER ASN GLU GLU TRP PHE LYS SEQRES 4 D 207 GLU LEU CYS PHE CYS ILE LEU THR ALA ASN PHE THR ALA SEQRES 5 D 207 GLU GLY GLY ILE ARG ILE GLN LYS GLU ILE GLY ASP GLY SEQRES 6 D 207 PHE LEU THR LEU PRO ARG GLU GLU LEU GLU GLU LYS LEU SEQRES 7 D 207 LYS ASN LEU GLY HIS ARG PHE TYR ARG LYS ARG ALA GLU SEQRES 8 D 207 TYR ILE VAL LEU ALA ARG ARG PHE LYS ASN ILE LYS ASP SEQRES 9 D 207 ILE VAL GLU SER PHE GLU ASN GLU LYS VAL ALA ARG GLU SEQRES 10 D 207 PHE LEU VAL ARG ASN ILE LYS GLY ILE GLY TYR GLN GLU SEQRES 11 D 207 ALA SER HIS PHE LEU ARG ASN VAL GLY TYR ASP ASP VAL SEQRES 12 D 207 ALA ILE ILE ASP ARG HIS ILE LEU ARG GLU LEU TYR GLU SEQRES 13 D 207 ASN ASN TYR ILE ASP GLU ILE PRO LYS THR LEU SER ARG SEQRES 14 D 207 ARG LYS TYR LEU GLU ILE GLU ASN ILE LEU ARG ASP ILE SEQRES 15 D 207 GLY GLU GLU VAL ASN LEU LYS LEU SER GLU LEU ASP LEU SEQRES 16 D 207 TYR ILE TRP TYR LEU ARG THR GLY LYS VAL LEU LYS SEQRES 1 E 15 DA DC DG DT DC DC DA 8OG DG DT DC DT DA SEQRES 2 E 15 DC DC SEQRES 1 F 15 DT DG DG DT DA DG DA DC DC DT DG DG DA SEQRES 2 F 15 DC DG SEQRES 1 G 15 DA DC DG DT DC DC DA 8OG DG DT DC DT DA SEQRES 2 G 15 DC DC SEQRES 1 H 15 DT DG DG DT DA DG DA DC DC DT DG DG DA SEQRES 2 H 15 DC DG SEQRES 1 I 15 DA DC DG DT DC DC DA 8OG DG DT DC DT DA SEQRES 2 I 15 DC DC SEQRES 1 J 15 DT DG DG DT DA DG DA DC DC DT DG DG DA SEQRES 2 J 15 DC DG SEQRES 1 K 15 DA DC DG DT DC DC DA 8OG DG DT DC DT DA SEQRES 2 K 15 DC DC SEQRES 1 L 15 DT DG DG DT DA DG DA DC DC DT DG DG DA SEQRES 2 L 15 DC DG MODRES 3KNT 8OG E 23 DG MODRES 3KNT 8OG G 23 DG MODRES 3KNT 8OG I 23 DG MODRES 3KNT 8OG K 23 DG HET 8OG E 23 23 HET 8OG G 23 23 HET 8OG I 23 23 HET 8OG K 23 23 HET NA A 208 1 HET NA B 208 1 HET NA C 208 1 HET NA D 208 1 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM NA SODIUM ION HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 5 8OG 4(C10 H14 N5 O8 P) FORMUL 13 NA 4(NA 1+) FORMUL 17 HOH *35(H2 O) HELIX 1 1 MET A 1 ASN A 12 1 12 HELIX 2 2 GLU A 14 SER A 28 1 15 HELIX 3 3 PHE A 29 LYS A 32 5 4 HELIX 4 4 SER A 33 ALA A 48 1 16 HELIX 5 5 THR A 51 GLY A 63 1 13 HELIX 6 6 ASP A 64 LEU A 67 5 4 HELIX 7 7 PRO A 70 LEU A 81 1 12 HELIX 8 8 ARG A 87 ALA A 96 1 10 HELIX 9 9 ARG A 97 LYS A 100 5 4 HELIX 10 10 ASN A 101 PHE A 109 1 9 HELIX 11 11 GLU A 112 ILE A 123 1 12 HELIX 12 12 TYR A 128 VAL A 138 1 11 HELIX 13 13 ASP A 147 ASN A 157 1 11 HELIX 14 14 SER A 168 GLU A 185 1 18 HELIX 15 15 LYS A 189 GLY A 203 1 15 HELIX 16 16 MET B 1 ASN B 12 1 12 HELIX 17 17 GLU B 14 SER B 28 1 15 HELIX 18 18 PHE B 29 ASN B 31 5 3 HELIX 19 19 SER B 33 ALA B 48 1 16 HELIX 20 20 THR B 51 GLY B 63 1 13 HELIX 21 21 ASP B 64 LEU B 69 1 6 HELIX 22 22 PRO B 70 GLY B 82 1 13 HELIX 23 23 PHE B 85 ARG B 97 1 13 HELIX 24 24 ARG B 98 LYS B 100 5 3 HELIX 25 25 ASN B 101 SER B 108 1 8 HELIX 26 26 ASN B 111 ILE B 123 1 13 HELIX 27 27 GLY B 127 VAL B 138 1 12 HELIX 28 28 ASP B 147 TYR B 155 1 9 HELIX 29 29 GLU B 156 ASN B 158 5 3 HELIX 30 30 SER B 168 ASN B 187 1 20 HELIX 31 31 LYS B 189 GLY B 203 1 15 HELIX 32 32 LEU C 3 SER C 13 1 11 HELIX 33 33 GLU C 14 SER C 28 1 15 HELIX 34 34 PHE C 29 LYS C 32 5 4 HELIX 35 35 SER C 33 LEU C 46 1 14 HELIX 36 36 THR C 51 GLY C 63 1 13 HELIX 37 37 ASP C 64 LEU C 69 1 6 HELIX 38 38 PRO C 70 LEU C 81 1 12 HELIX 39 39 PHE C 85 ALA C 96 1 12 HELIX 40 40 ARG C 97 LYS C 100 5 4 HELIX 41 41 ASN C 101 PHE C 109 1 9 HELIX 42 42 ASN C 111 ILE C 123 1 13 HELIX 43 43 GLY C 127 VAL C 138 1 12 HELIX 44 44 ASP C 147 ASN C 157 1 11 HELIX 45 45 SER C 168 ASN C 187 1 20 HELIX 46 46 LYS C 189 GLY C 203 1 15 HELIX 47 47 MET D 2 SER D 13 1 12 HELIX 48 48 ILE D 15 SER D 28 1 14 HELIX 49 49 PHE D 29 LYS D 32 5 4 HELIX 50 50 SER D 33 ALA D 48 1 16 HELIX 51 51 THR D 51 GLY D 63 1 13 HELIX 52 52 ASP D 64 THR D 68 5 5 HELIX 53 53 PRO D 70 LEU D 81 1 12 HELIX 54 54 PHE D 85 ARG D 97 1 13 HELIX 55 55 ARG D 98 LYS D 100 5 3 HELIX 56 56 ASN D 101 GLU D 107 1 7 HELIX 57 57 ASN D 111 ILE D 123 1 13 HELIX 58 58 GLY D 127 VAL D 138 1 12 HELIX 59 59 ASP D 147 ASN D 157 1 11 HELIX 60 60 SER D 168 VAL D 186 1 19 HELIX 61 61 LYS D 189 THR D 202 1 14 LINK O3' DA E 22 P 8OG E 23 1555 1555 1.61 LINK O3' 8OG E 23 P DG E 24 1555 1555 1.60 LINK O3' DA G 22 P 8OG G 23 1555 1555 1.61 LINK O3' 8OG G 23 P DG G 24 1555 1555 1.60 LINK O3' DA I 22 P 8OG I 23 1555 1555 1.61 LINK O3' 8OG I 23 P DG I 24 1555 1555 1.60 LINK O3' DA K 22 P 8OG K 23 1555 1555 1.61 LINK O3' 8OG K 23 P DG K 24 1555 1555 1.60 LINK O VAL A 120 NA NA A 208 1555 1555 2.29 LINK O ILE A 123 NA NA A 208 1555 1555 2.25 LINK O ILE A 126 NA NA A 208 1555 1555 2.33 LINK NA NA A 208 OP1 DC E 26 1555 1555 2.87 LINK O VAL B 120 NA NA B 208 1555 1555 2.56 LINK O ILE B 123 NA NA B 208 1555 1555 2.50 LINK O ILE B 126 NA NA B 208 1555 1555 2.41 LINK NA NA B 208 OP1 DC G 26 1555 1555 2.93 LINK O VAL C 120 NA NA C 208 1555 1555 2.28 LINK O ILE C 123 NA NA C 208 1555 1555 2.29 LINK O ILE C 126 NA NA C 208 1555 1555 2.30 LINK NA NA C 208 OP1 DC I 26 1555 1555 2.32 LINK O VAL D 120 NA NA D 208 1555 1555 2.16 LINK O ILE D 123 NA NA D 208 1555 1555 2.25 LINK O ILE D 126 NA NA D 208 1555 1555 2.26 LINK NA NA D 208 OP1 DC K 26 1555 1555 2.25 SITE 1 AC1 4 VAL A 120 ILE A 123 ILE A 126 DC E 26 SITE 1 AC2 4 VAL B 120 ILE B 123 ILE B 126 DC G 26 SITE 1 AC3 4 VAL C 120 ILE C 123 ILE C 126 DC I 26 SITE 1 AC4 4 VAL D 120 ILE D 123 ILE D 126 DC K 26 CRYST1 54.800 150.030 90.270 90.00 107.53 90.00 P 1 21 1 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 0.018248 0.000000 0.005764 0.00000 SCALE2 0.000000 0.006665 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011617 0.00000