HEADER LYASE 14-NOV-24 9KL8 TITLE CO-CRYSTAL STRUCTURE OF HUMAN 8-OXOGUANINE GLYCOSYLASE N149C MUTANT TITLE 2 WITH DNA CONTAINING PHOTOCAGED 8-OXOGUANINE AFTER DEPROTECTION 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; COMPND 14 MUTATION: 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, KEYWDS 2 DEPROTECTION OF 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 9KL8 1 JRNL REVDAT 1 23-JUL-25 9KL8 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. 2.48 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) : 2.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 19404 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.290 REMARK 3 FREE R VALUE TEST SET COUNT : 1414 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 42.0100 - 5.3400 1.00 1992 149 0.2146 0.2323 REMARK 3 2 5.3400 - 4.2400 1.00 1834 157 0.1685 0.1886 REMARK 3 3 4.2400 - 3.7000 1.00 1806 154 0.1709 0.2257 REMARK 3 4 3.7000 - 3.3700 1.00 1806 129 0.2117 0.2610 REMARK 3 5 3.3700 - 3.1200 1.00 1776 147 0.2267 0.3017 REMARK 3 6 3.1200 - 2.9400 1.00 1780 131 0.2495 0.3106 REMARK 3 7 2.9400 - 2.7900 1.00 1782 128 0.2669 0.3295 REMARK 3 8 2.7900 - 2.6700 1.00 1731 152 0.2759 0.2854 REMARK 3 9 2.6700 - 2.5700 0.99 1751 137 0.2861 0.3730 REMARK 3 10 2.5700 - 2.4800 0.99 1732 130 0.3423 0.3814 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) : 0.304 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.786 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 54.13 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 70.99 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 : 0.002 2966 REMARK 3 ANGLE : 0.477 4130 REMARK 3 CHIRALITY : 0.037 452 REMARK 3 PLANARITY : 0.005 467 REMARK 3 DIHEDRAL : 19.885 550 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 11:92) REMARK 3 ORIGIN FOR THE GROUP (A): 13.3404 18.7157 -6.0534 REMARK 3 T TENSOR REMARK 3 T11: 0.5677 T22: 0.4476 REMARK 3 T33: 0.4124 T12: -0.0159 REMARK 3 T13: 0.0292 T23: 0.0463 REMARK 3 L TENSOR REMARK 3 L11: 1.9690 L22: 1.2750 REMARK 3 L33: 2.2574 L12: 0.0638 REMARK 3 L13: 0.3593 L23: -0.4748 REMARK 3 S TENSOR REMARK 3 S11: 0.0096 S12: 0.2894 S13: -0.0956 REMARK 3 S21: -0.4667 S22: -0.1235 S23: 0.1574 REMARK 3 S31: 0.2998 S32: 0.2763 S33: 0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 93:192) REMARK 3 ORIGIN FOR THE GROUP (A): -0.7954 21.7029 -2.1664 REMARK 3 T TENSOR REMARK 3 T11: 0.4070 T22: 0.3599 REMARK 3 T33: 0.4142 T12: -0.0565 REMARK 3 T13: -0.0216 T23: 0.0128 REMARK 3 L TENSOR REMARK 3 L11: 1.1326 L22: 0.7647 REMARK 3 L33: 1.7943 L12: -0.8282 REMARK 3 L13: 0.1636 L23: -0.6928 REMARK 3 S TENSOR REMARK 3 S11: 0.0789 S12: -0.0026 S13: 0.0251 REMARK 3 S21: -0.1697 S22: -0.0550 S23: -0.0411 REMARK 3 S31: 0.1460 S32: 0.1311 S33: 0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 193:261) REMARK 3 ORIGIN FOR THE GROUP (A): -14.1110 16.7926 3.6238 REMARK 3 T TENSOR REMARK 3 T11: 0.3899 T22: 0.3166 REMARK 3 T33: 0.4147 T12: 0.0206 REMARK 3 T13: -0.0278 T23: 0.0484 REMARK 3 L TENSOR REMARK 3 L11: 2.5698 L22: 1.1297 REMARK 3 L33: 0.6957 L12: 0.1101 REMARK 3 L13: -0.1743 L23: -0.7097 REMARK 3 S TENSOR REMARK 3 S11: -0.0607 S12: -0.0953 S13: 0.2072 REMARK 3 S21: 0.0104 S22: 0.0380 S23: 0.2874 REMARK 3 S31: -0.1607 S32: -0.1361 S33: 0.0001 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 262:323) REMARK 3 ORIGIN FOR THE GROUP (A): -15.3184 35.4164 -9.8098 REMARK 3 T TENSOR REMARK 3 T11: 0.4604 T22: 0.5239 REMARK 3 T33: 0.5565 T12: 0.0274 REMARK 3 T13: 0.0140 T23: 0.0219 REMARK 3 L TENSOR REMARK 3 L11: 1.5038 L22: 0.2953 REMARK 3 L33: 1.2701 L12: -0.3822 REMARK 3 L13: -0.5414 L23: -0.3671 REMARK 3 S TENSOR REMARK 3 S11: 0.2005 S12: -0.2446 S13: 0.4216 REMARK 3 S21: -0.1420 S22: -0.1397 S23: 0.1504 REMARK 3 S31: -0.1408 S32: -0.4489 S33: -0.0001 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN B AND RESID 1:4) REMARK 3 ORIGIN FOR THE GROUP (A): -31.6675 34.8286 6.0199 REMARK 3 T TENSOR REMARK 3 T11: 2.0027 T22: 4.1202 REMARK 3 T33: 2.8241 T12: 1.0436 REMARK 3 T13: -0.2281 T23: 0.3224 REMARK 3 L TENSOR REMARK 3 L11: 0.0173 L22: 0.0229 REMARK 3 L33: 0.0645 L12: -0.0164 REMARK 3 L13: 0.0194 L23: -0.0370 REMARK 3 S TENSOR REMARK 3 S11: -0.7822 S12: -0.2633 S13: 0.3811 REMARK 3 S21: 0.7393 S22: -1.0395 S23: -0.2950 REMARK 3 S31: -0.8194 S32: -0.5454 S33: -0.0006 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN B AND RESID 5:11) REMARK 3 ORIGIN FOR THE GROUP (A): -13.2425 33.4346 17.4473 REMARK 3 T TENSOR REMARK 3 T11: 1.2597 T22: 1.1203 REMARK 3 T33: 0.9624 T12: 0.0825 REMARK 3 T13: -0.2908 T23: -0.2277 REMARK 3 L TENSOR REMARK 3 L11: 0.1506 L22: 4.6824 REMARK 3 L33: 0.0682 L12: -0.8470 REMARK 3 L13: 0.0992 L23: -0.5248 REMARK 3 S TENSOR REMARK 3 S11: -0.8771 S12: 0.3956 S13: 0.9509 REMARK 3 S21: 0.7749 S22: 0.1591 S23: 1.1940 REMARK 3 S31: -2.1782 S32: -0.1853 S33: -0.2056 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN C AND RESID 22:25) REMARK 3 ORIGIN FOR THE GROUP (A): -12.8268 31.7812 5.8768 REMARK 3 T TENSOR REMARK 3 T11: 1.1156 T22: 0.6438 REMARK 3 T33: 0.6966 T12: -0.1724 REMARK 3 T13: 0.1341 T23: -0.0891 REMARK 3 L TENSOR REMARK 3 L11: 0.0189 L22: 1.6137 REMARK 3 L33: 1.0586 L12: -0.1834 REMARK 3 L13: 0.1488 L23: -1.3099 REMARK 3 S TENSOR REMARK 3 S11: 0.6878 S12: -0.5014 S13: 0.6233 REMARK 3 S21: -0.9977 S22: 0.2905 S23: 0.6047 REMARK 3 S31: -3.0980 S32: 0.3246 S33: 0.2650 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN C AND RESID 26:29) REMARK 3 ORIGIN FOR THE GROUP (A): -28.5559 28.0048 12.7060 REMARK 3 T TENSOR REMARK 3 T11: 0.7679 T22: 1.3551 REMARK 3 T33: 1.6872 T12: 0.2549 REMARK 3 T13: 0.3545 T23: -0.0353 REMARK 3 L TENSOR REMARK 3 L11: 0.0804 L22: 0.0204 REMARK 3 L33: 0.4486 L12: -0.0423 REMARK 3 L13: 0.1892 L23: -0.0979 REMARK 3 S TENSOR REMARK 3 S11: -0.2289 S12: 0.5245 S13: -0.0465 REMARK 3 S21: 0.8145 S22: -0.3240 S23: 2.1291 REMARK 3 S31: 0.2500 S32: -1.2651 S33: 0.0857 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 9KL8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-NOV-24. REMARK 100 THE DEPOSITION ID IS D_1300053783. 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 : 19518 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.480 REMARK 200 RESOLUTION RANGE LOW (A) : 42.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 157.0 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.7600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 156.0 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.620 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 (%): 52.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 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 141.84667 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 70.92333 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 106.38500 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 35.46167 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 177.30833 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 141.84667 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 70.92333 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 35.46167 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 106.38500 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 177.30833 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: 4250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -74.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 CA CA A 407 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 509 LIES ON A SPECIAL POSITION. 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 DT B 3 C1' N1 C2 O2 N3 C4 O4 REMARK 470 DT B 3 C5 C7 C6 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 ASP A 81 CG OD1 OD2 REMARK 470 LYS A 82 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 GLN A 121 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 LYS A 198 NZ 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 CB CG CD OE1 NE2 REMARK 470 LYS A 289 CG CD CE NZ REMARK 470 LYS A 297 CD CE NZ REMARK 470 SER A 320 OG REMARK 470 LEU A 323 CD1 CD2 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 NE2 GLN A 315 O HOH A 501 2.10 REMARK 500 O GLY A 312 O HOH A 501 2.17 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 CYS A 28 112.49 -163.59 REMARK 500 THR A 69 -147.23 -96.24 REMARK 500 LEU A 170 -76.36 -101.29 REMARK 500 ASP A 174 -131.91 55.59 REMARK 500 ASP A 175 30.45 -99.16 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 565 DISTANCE = 9.57 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 175.7 REMARK 620 3 LEU A 243 O 84.7 99.1 REMARK 620 4 VAL A 246 O 90.1 92.0 88.0 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9KKY RELATED DB: PDB REMARK 900 9KKY IS THE CO-CRYSTAL STRUCTURE BEFORE DEPROTECTION OF THE REMARK 900 PHOTOCAGED GROUP DBREF 9KL8 B 0 15 PDB 9KL8 9KL8 0 15 DBREF 9KL8 C 15 30 PDB 9KL8 9KL8 15 30 DBREF 9KL8 A 11 327 UNP O15527 OGG1_HUMAN 11 327 SEQADV 9KL8 MET A -9 UNP O15527 INITIATING METHIONINE SEQADV 9KL8 GLY A -8 UNP O15527 EXPRESSION TAG SEQADV 9KL8 SER A -7 UNP O15527 EXPRESSION TAG SEQADV 9KL8 SER A -6 UNP O15527 EXPRESSION TAG SEQADV 9KL8 HIS A -5 UNP O15527 EXPRESSION TAG SEQADV 9KL8 HIS A -4 UNP O15527 EXPRESSION TAG SEQADV 9KL8 HIS A -3 UNP O15527 EXPRESSION TAG SEQADV 9KL8 HIS A -2 UNP O15527 EXPRESSION TAG SEQADV 9KL8 HIS A -1 UNP O15527 EXPRESSION TAG SEQADV 9KL8 HIS A 0 UNP O15527 EXPRESSION TAG SEQADV 9KL8 SER A 1 UNP O15527 EXPRESSION TAG SEQADV 9KL8 SER A 2 UNP O15527 EXPRESSION TAG SEQADV 9KL8 GLY A 3 UNP O15527 EXPRESSION TAG SEQADV 9KL8 LEU A 4 UNP O15527 EXPRESSION TAG SEQADV 9KL8 VAL A 5 UNP O15527 EXPRESSION TAG SEQADV 9KL8 PRO A 6 UNP O15527 EXPRESSION TAG SEQADV 9KL8 ARG A 7 UNP O15527 EXPRESSION TAG SEQADV 9KL8 GLY A 8 UNP O15527 EXPRESSION TAG SEQADV 9KL8 SER A 9 UNP O15527 EXPRESSION TAG SEQADV 9KL8 HIS A 10 UNP O15527 EXPRESSION TAG SEQADV 9KL8 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 23 HET CA C 101 1 HET CA A 401 1 HET GOL A 402 6 HET GOL A 403 6 HET CA A 404 1 HET CA A 405 1 HET CA A 406 1 HET CA A 407 1 HET CA A 408 1 HET CA A 409 1 HET CA A 410 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 9(CA 2+) FORMUL 6 GOL 2(C3 H8 O3) FORMUL 15 HOH *69(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 ARG A 79 SER A 83 5 5 HELIX 4 AA4 THR A 89 GLN A 101 1 13 HELIX 5 AA5 THR A 105 VAL A 116 1 12 HELIX 6 AA6 ASP A 117 GLN A 125 1 9 HELIX 7 AA7 ASP A 136 CYS A 146 1 11 HELIX 8 AA8 ASN A 151 GLY A 167 1 17 HELIX 9 AA9 SER A 183 ALA A 188 1 6 HELIX 10 AB1 GLU A 191 LYS A 198 1 8 HELIX 11 AB2 LEU A 199 GLY A 200 5 2 HELIX 12 AB3 LEU A 201 GLY A 202 5 2 HELIX 13 AB4 TYR A 203 GLN A 219 1 17 HELIX 14 AB5 GLY A 221 GLN A 227 1 7 HELIX 15 AB6 LEU A 228 GLU A 230 5 3 HELIX 16 AB7 SER A 232 CYS A 241 1 10 HELIX 17 AB8 GLY A 247 LEU A 259 1 13 HELIX 18 AB9 ASP A 268 ASP A 278 1 11 HELIX 19 AC1 SER A 292 GLY A 308 1 17 HELIX 20 AC2 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 TYR A 78 -1 O CYS A 75 N ALA A 24 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 LEU A 59 O GLN A 62 SHEET 5 AA1 5 TRP A 47 SER A 51 -1 N SER A 51 O HIS A 54 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 A DG C 24 1555 1555 1.61 LINK OP1 DC C 26 CA CA A 401 1555 1555 2.53 LINK OD1 ASP A 61 CA CA A 404 1555 1555 3.00 LINK O CYS A 241 CA CA A 401 1555 1555 2.39 LINK O LEU A 243 CA CA A 401 1555 1555 2.53 LINK O VAL A 246 CA CA A 401 1555 1555 2.77 CRYST1 91.460 91.460 212.770 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 0.010934 0.006313 0.000000 0.00000 SCALE2 0.000000 0.012625 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004700 0.00000 CONECT 217 230 CONECT 230 217 231 232 233 CONECT 231 230 CONECT 232 230 CONECT 233 230 234 CONECT 234 233 235 CONECT 235 234 236 237 CONECT 236 235 240 CONECT 237 235 238 239 CONECT 238 237 253 CONECT 239 237 240 CONECT 240 236 239 241 CONECT 241 240 242 251 CONECT 242 241 243 252 CONECT 243 242 244 CONECT 244 243 245 251 CONECT 245 244 246 247 CONECT 246 245 CONECT 247 245 248 CONECT 248 247 249 250 CONECT 249 248 CONECT 250 248 251 CONECT 251 241 244 250 CONECT 252 242 CONECT 253 238 CONECT 318 2841 CONECT 810 2854 CONECT 2216 2841 CONECT 2230 2841 CONECT 2249 2841 CONECT 2841 318 2216 2230 2249 CONECT 2842 2843 2844 CONECT 2843 2842 CONECT 2844 2842 2845 2846 CONECT 2845 2844 CONECT 2846 2844 2847 CONECT 2847 2846 CONECT 2848 2849 2850 CONECT 2849 2848 CONECT 2850 2848 2851 2852 CONECT 2851 2850 CONECT 2852 2850 2853 CONECT 2853 2852 CONECT 2854 810 MASTER 503 0 12 20 7 0 0 6 2868 3 44 30 END