HEADER LYASE 14-NOV-24 9KKY TITLE CO-CRYSTAL STRUCTURE OF HUMAN 8-OXOGUANINE GLYCOSYLASE N149C MUTANT TITLE 2 WITH DNA CONTAINING PHOTOCAGED 8-OXOGUANINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*G)-3'); COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*AP*(8OG)P*GP*TP*CP*TP*AP*C)-3'); COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: N-GLYCOSYLASE/DNA LYASE; COMPND 11 CHAIN: A; COMPND 12 EC: 3.2.2.-,4.2.99.18; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: OGG1, MMH, MUTM, OGH1; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS DNA-GLYCOSYLASE, DNA REPAIR, BASE EXCISION REPAIR, HOGG1, PHOTOCAGED, KEYWDS 2 O6-(O-NITROPHENISOPROPYL) 8-OXOGUANINE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR T.IMURA,K.-C.YANG,Y.HOSOKAWA,H.-Y.SHIH,Y.BAN,J.YAMAMOTO,M.MAESTRE- AUTHOR 2 REYNA REVDAT 2 10-SEP-25 9KKY 1 JRNL REVDAT 1 23-JUL-25 9KKY 0 JRNL AUTH T.IMURA,Y.HOSOKAWA,K.C.YANG,Y.BAN,H.Y.SHIH,J.YAMAMOTO, JRNL AUTH 2 M.MAESTRE-REYNA JRNL TITL REVISITING THE CO-CRYSTAL STRUCTURE OF A DNA GLYCOSYLASE JRNL TITL 2 WITH PHOTOCAGED SUBSTRATE: A SUITABLE TIME-RESOLVED JRNL TITL 3 CRYSTALLOGRAPHY TARGET? JRNL REF IUCRJ V. 12 515 2025 JRNL REFN ESSN 2052-2525 JRNL PMID 40658017 JRNL DOI 10.1107/S2052252525006062 REMARK 2 REMARK 2 RESOLUTION. 2.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 12734 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.220 REMARK 3 FREE R VALUE TEST SET COUNT : 920 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 29.3500 - 5.3700 0.97 1819 131 0.2175 0.2468 REMARK 3 2 5.3700 - 4.2600 0.98 1692 149 0.1917 0.2245 REMARK 3 3 4.2600 - 3.7300 0.97 1651 144 0.1915 0.2451 REMARK 3 4 3.7200 - 3.3900 0.98 1678 115 0.2291 0.2454 REMARK 3 5 3.3900 - 3.1400 0.99 1669 130 0.2731 0.3149 REMARK 3 6 3.1400 - 2.9600 0.99 1649 129 0.3121 0.4012 REMARK 3 7 2.9600 - 2.8100 1.00 1656 122 0.3158 0.3813 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.339 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.072 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 69.03 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 85.19 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 : 0.008 2888 REMARK 3 ANGLE : 1.242 4021 REMARK 3 CHIRALITY : 0.088 446 REMARK 3 PLANARITY : 0.009 456 REMARK 3 DIHEDRAL : 20.583 1039 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.3940 33.6489 13.3038 REMARK 3 T TENSOR REMARK 3 T11: 1.8104 T22: 1.6230 REMARK 3 T33: 1.7617 T12: 0.2826 REMARK 3 T13: -0.4390 T23: -0.2729 REMARK 3 L TENSOR REMARK 3 L11: 7.3377 L22: 2.1062 REMARK 3 L33: 8.1810 L12: -2.6602 REMARK 3 L13: 0.0295 L23: 0.2844 REMARK 3 S TENSOR REMARK 3 S11: -1.4712 S12: -0.0303 S13: 2.2180 REMARK 3 S21: -0.0924 S22: 0.1675 S23: 1.0633 REMARK 3 S31: -1.7932 S32: -1.4910 S33: 1.2662 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 22 THROUGH 29 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.5888 29.5989 9.8393 REMARK 3 T TENSOR REMARK 3 T11: 1.4630 T22: 1.4157 REMARK 3 T33: 1.1571 T12: -0.0219 REMARK 3 T13: 0.0300 T23: -0.0884 REMARK 3 L TENSOR REMARK 3 L11: 5.8279 L22: 4.3484 REMARK 3 L33: 4.3629 L12: -4.6277 REMARK 3 L13: 4.9642 L23: -3.6386 REMARK 3 S TENSOR REMARK 3 S11: 0.0740 S12: -0.6716 S13: 1.2322 REMARK 3 S21: 0.4664 S22: -0.4200 S23: 1.1865 REMARK 3 S31: -2.7180 S32: 0.4520 S33: 0.4573 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 11 THROUGH 329 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.0192 22.1610 -3.2845 REMARK 3 T TENSOR REMARK 3 T11: 0.8045 T22: 0.5782 REMARK 3 T33: 0.3008 T12: -0.0037 REMARK 3 T13: -0.0744 T23: -0.0186 REMARK 3 L TENSOR REMARK 3 L11: 2.4495 L22: 0.3678 REMARK 3 L33: 2.3325 L12: 0.0779 REMARK 3 L13: -0.1603 L23: -0.4674 REMARK 3 S TENSOR REMARK 3 S11: -0.0689 S12: -0.0794 S13: 0.2703 REMARK 3 S21: -0.1112 S22: -0.0519 S23: -0.0078 REMARK 3 S31: -0.1659 S32: 0.1109 S33: 0.1197 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 9KKY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-NOV-24. REMARK 100 THE DEPOSITION ID IS D_1300053407. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-DEC-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6-6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : TPS 07A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976254 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14869 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 4.527 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.87 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.830 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: 1YQR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, CALCIUM CHLORIDE, SODIUM REMARK 280 CACODYLATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 141.17733 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 70.58867 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 105.88300 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 35.29433 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 176.47167 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 141.17733 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 70.58867 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 35.29433 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 105.88300 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 176.47167 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, 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 DT B 0 REMARK 465 DA B 12 REMARK 465 DC B 13 REMARK 465 DG B 14 REMARK 465 DC B 15 REMARK 465 DA C 15 REMARK 465 DG C 16 REMARK 465 DC C 17 REMARK 465 DG C 18 REMARK 465 DT C 19 REMARK 465 DC C 20 REMARK 465 DC C 21 REMARK 465 DC C 30 REMARK 465 MET A -9 REMARK 465 GLY A -8 REMARK 465 SER A -7 REMARK 465 SER A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 SER A 1 REMARK 465 SER A 2 REMARK 465 GLY A 3 REMARK 465 LEU A 4 REMARK 465 VAL A 5 REMARK 465 PRO A 6 REMARK 465 ARG A 7 REMARK 465 GLY A 8 REMARK 465 SER A 9 REMARK 465 HIS A 10 REMARK 465 ARG A 324 REMARK 465 GLN A 325 REMARK 465 SER A 326 REMARK 465 ARG A 327 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 B 11 C8 N7 C5 C6 O6 N1 C2 REMARK 470 DG B 11 N2 N3 C4 REMARK 470 DA C 22 P OP1 OP2 REMARK 470 8OG C 23 C8 N7 C5 C6 O6 N1 C2 REMARK 470 8OG C 23 N2 N3 C4 O8 REMARK 470 GLU A 71 CG CD OE1 OE2 REMARK 470 ARG A 79 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 81 CG OD1 OD2 REMARK 470 LYS A 82 CG CD CE NZ REMARK 470 SER A 83 OG REMARK 470 GLN A 84 CG CD OE1 NE2 REMARK 470 LYS A 98 CG CD CE NZ REMARK 470 SER A 118 OG REMARK 470 GLN A 121 CB CG CD OE1 NE2 REMARK 470 GLU A 122 CG CD OE1 OE2 REMARK 470 GLN A 125 CG CD OE1 NE2 REMARK 470 LYS A 126 CG CD CE NZ REMARK 470 SER A 148 OG REMARK 470 ASN A 151 CG OD1 ND2 REMARK 470 ARG A 154 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 206 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 234 CG CD OE1 OE2 REMARK 470 GLU A 235 CD OE1 OE2 REMARK 470 ARG A 277 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 282 CG ND1 CD2 CE1 NE2 REMARK 470 SER A 286 OG REMARK 470 GLN A 287 CG CD OE1 NE2 REMARK 470 LYS A 289 CG CD CE NZ REMARK 470 GLN A 294 CG CD OE1 NE2 REMARK 470 LYS A 297 CD CE NZ REMARK 470 SER A 320 OG REMARK 470 LEU A 323 CG CD1 CD2 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 DA C 22 O4' - C1' - N9 ANGL. DEV. = 1.8 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 GLN A 43 -66.30 -102.64 REMARK 500 THR A 69 -167.10 -101.95 REMARK 500 CYS A 149 66.57 34.41 REMARK 500 LEU A 170 -70.07 -97.94 REMARK 500 ASP A 174 -121.50 54.87 REMARK 500 ASP A 322 -89.30 -81.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 549 DISTANCE = 6.46 ANGSTROMS REMARK 525 HOH A 551 DISTANCE = 7.38 ANGSTROMS 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 CA A 401 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC C 26 OP1 REMARK 620 2 CYS A 241 O 171.3 REMARK 620 3 LEU A 243 O 92.3 96.1 REMARK 620 4 VAL A 246 O 95.5 86.8 91.1 REMARK 620 N 1 2 3 DBREF 9KKY B 0 15 PDB 9KKY 9KKY 0 15 DBREF 9KKY C 15 30 PDB 9KKY 9KKY 15 30 DBREF 9KKY A 11 327 UNP O15527 OGG1_HUMAN 11 327 SEQADV 9KKY MET A -9 UNP O15527 INITIATING METHIONINE SEQADV 9KKY GLY A -8 UNP O15527 EXPRESSION TAG SEQADV 9KKY SER A -7 UNP O15527 EXPRESSION TAG SEQADV 9KKY SER A -6 UNP O15527 EXPRESSION TAG SEQADV 9KKY HIS A -5 UNP O15527 EXPRESSION TAG SEQADV 9KKY HIS A -4 UNP O15527 EXPRESSION TAG SEQADV 9KKY HIS A -3 UNP O15527 EXPRESSION TAG SEQADV 9KKY HIS A -2 UNP O15527 EXPRESSION TAG SEQADV 9KKY HIS A -1 UNP O15527 EXPRESSION TAG SEQADV 9KKY HIS A 0 UNP O15527 EXPRESSION TAG SEQADV 9KKY SER A 1 UNP O15527 EXPRESSION TAG SEQADV 9KKY SER A 2 UNP O15527 EXPRESSION TAG SEQADV 9KKY GLY A 3 UNP O15527 EXPRESSION TAG SEQADV 9KKY LEU A 4 UNP O15527 EXPRESSION TAG SEQADV 9KKY VAL A 5 UNP O15527 EXPRESSION TAG SEQADV 9KKY PRO A 6 UNP O15527 EXPRESSION TAG SEQADV 9KKY ARG A 7 UNP O15527 EXPRESSION TAG SEQADV 9KKY GLY A 8 UNP O15527 EXPRESSION TAG SEQADV 9KKY SER A 9 UNP O15527 EXPRESSION TAG SEQADV 9KKY HIS A 10 UNP O15527 EXPRESSION TAG SEQADV 9KKY CYS A 149 UNP O15527 ASN 149 ENGINEERED MUTATION SEQRES 1 B 16 DT DG DG DT DA DG DA DC DC DT DG DG DA SEQRES 2 B 16 DC DG DC SEQRES 1 C 16 DA DG DC DG DT DC DC DA 8OG DG DT DC DT SEQRES 2 C 16 DA DC DC SEQRES 1 A 337 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 337 LEU VAL PRO ARG GLY SER HIS MET GLY HIS ARG THR LEU SEQRES 3 A 337 ALA SER THR PRO ALA LEU TRP ALA SER ILE PRO CYS PRO SEQRES 4 A 337 ARG SER GLU LEU ARG LEU ASP LEU VAL LEU PRO SER GLY SEQRES 5 A 337 GLN SER PHE ARG TRP ARG GLU GLN SER PRO ALA HIS TRP SEQRES 6 A 337 SER GLY VAL LEU ALA ASP GLN VAL TRP THR LEU THR GLN SEQRES 7 A 337 THR GLU GLU GLN LEU HIS CYS THR VAL TYR ARG GLY ASP SEQRES 8 A 337 LYS SER GLN ALA SER ARG PRO THR PRO ASP GLU LEU GLU SEQRES 9 A 337 ALA VAL ARG LYS TYR PHE GLN LEU ASP VAL THR LEU ALA SEQRES 10 A 337 GLN LEU TYR HIS HIS TRP GLY SER VAL ASP SER HIS PHE SEQRES 11 A 337 GLN GLU VAL ALA GLN LYS PHE GLN GLY VAL ARG LEU LEU SEQRES 12 A 337 ARG GLN ASP PRO ILE GLU CYS LEU PHE SER PHE ILE CYS SEQRES 13 A 337 SER SER CYS ASN ASN ILE ALA ARG ILE THR GLY MET VAL SEQRES 14 A 337 GLU ARG LEU CYS GLN ALA PHE GLY PRO ARG LEU ILE GLN SEQRES 15 A 337 LEU ASP ASP VAL THR TYR HIS GLY PHE PRO SER LEU GLN SEQRES 16 A 337 ALA LEU ALA GLY PRO GLU VAL GLU ALA HIS LEU ARG LYS SEQRES 17 A 337 LEU GLY LEU GLY TYR ARG ALA ARG TYR VAL SER ALA SER SEQRES 18 A 337 ALA ARG ALA ILE LEU GLU GLU GLN GLY GLY LEU ALA TRP SEQRES 19 A 337 LEU GLN GLN LEU ARG GLU SER SER TYR GLU GLU ALA HIS SEQRES 20 A 337 LYS ALA LEU CYS ILE LEU PRO GLY VAL GLY THR LYS VAL SEQRES 21 A 337 ALA ASP CYS ILE CYS LEU MET ALA LEU ASP LYS PRO GLN SEQRES 22 A 337 ALA VAL PRO VAL ASP VAL HIS MET TRP HIS ILE ALA GLN SEQRES 23 A 337 ARG ASP TYR SER TRP HIS PRO THR THR SER GLN ALA LYS SEQRES 24 A 337 GLY PRO SER PRO GLN THR ASN LYS GLU LEU GLY ASN PHE SEQRES 25 A 337 PHE ARG SER LEU TRP GLY PRO TYR ALA GLY TRP ALA GLN SEQRES 26 A 337 ALA VAL LEU PHE SER ALA ASP LEU ARG GLN SER ARG HET 8OG C 23 12 HET CA A 401 1 HET GOL A 402 6 HET CA A 403 1 HET CA A 404 1 HET CA A 405 1 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM CA CALCIUM ION HETNAM GOL GLYCEROL HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 8OG C10 H14 N5 O8 P FORMUL 4 CA 4(CA 2+) FORMUL 5 GOL C3 H8 O3 FORMUL 9 HOH *49(H2 O) HELIX 1 AA1 THR A 19 TRP A 23 5 5 HELIX 2 AA2 ARG A 34 LEU A 39 1 6 HELIX 3 AA3 THR A 89 GLN A 101 1 13 HELIX 4 AA4 THR A 105 VAL A 116 1 12 HELIX 5 AA5 ASP A 117 GLN A 125 1 9 HELIX 6 AA6 ASP A 136 CYS A 146 1 11 HELIX 7 AA7 ASN A 151 GLY A 167 1 17 HELIX 8 AA8 SER A 183 ALA A 188 1 6 HELIX 9 AA9 GLU A 191 LEU A 199 1 9 HELIX 10 AB1 TYR A 203 GLU A 218 1 16 HELIX 11 AB2 GLY A 221 GLN A 227 1 7 HELIX 12 AB3 SER A 232 CYS A 241 1 10 HELIX 13 AB4 GLY A 247 LEU A 259 1 13 HELIX 14 AB5 ASP A 268 ASP A 278 1 11 HELIX 15 AB6 SER A 292 GLY A 308 1 17 HELIX 16 AB7 TYR A 310 LEU A 323 1 14 SHEET 1 AA1 5 ALA A 24 PRO A 27 0 SHEET 2 AA1 5 GLN A 72 VAL A 77 -1 O LEU A 73 N ILE A 26 SHEET 3 AA1 5 GLN A 62 GLN A 68 -1 N THR A 67 O HIS A 74 SHEET 4 AA1 5 HIS A 54 LEU A 59 -1 N TRP A 55 O LEU A 66 SHEET 5 AA1 5 ARG A 48 SER A 51 -1 N ARG A 48 O SER A 56 SHEET 1 AA2 2 ARG A 169 LEU A 173 0 SHEET 2 AA2 2 VAL A 176 HIS A 179 -1 O TYR A 178 N LEU A 170 LINK O3' DA C 22 P 8OG C 23 1555 1555 1.61 LINK O3' 8OG C 23 P DG C 24 1555 1555 1.61 LINK OP1 DC C 26 CA CA A 401 1555 1555 2.23 LINK O CYS A 241 CA CA A 401 1555 1555 2.29 LINK O LEU A 243 CA CA A 401 1555 1555 2.50 LINK O VAL A 246 CA CA A 401 1555 1555 2.62 CRYST1 89.673 89.673 211.766 90.00 90.00 120.00 P 65 2 2 12 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 0.011152 0.006438 0.000000 0.00000 SCALE2 0.000000 0.012877 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004722 0.00000 CONECT 227 240 CONECT 240 227 241 242 243 CONECT 241 240 CONECT 242 240 CONECT 243 240 244 CONECT 244 243 245 CONECT 245 244 246 247 CONECT 246 245 250 CONECT 247 245 248 249 CONECT 248 247 252 CONECT 249 247 250 CONECT 250 246 249 251 CONECT 251 250 CONECT 252 248 CONECT 295 2773 CONECT 2163 2773 CONECT 2177 2773 CONECT 2196 2773 CONECT 2773 295 2163 2177 2196 CONECT 2774 2775 2776 CONECT 2775 2774 CONECT 2776 2774 2777 2778 CONECT 2777 2776 CONECT 2778 2776 2779 CONECT 2779 2778 MASTER 426 0 6 16 7 0 0 6 2811 3 25 30 END