HEADER HYDROLASE 18-OCT-18 6ILI TITLE CRYSTAL STRUCTURE OF HUMAN MTH1(G2K/D120N MUTANT) IN COMPLEX WITH 8- TITLE 2 OXO-DGTP AT PH 6.5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 2-HYDROXY-DATP DIPHOSPHATASE,8-OXO-DGTPASE,NUCLEOSIDE COMPND 5 DIPHOSPHATE-LINKED MOIETY X MOTIF 1,NUDIX MOTIF 1; COMPND 6 EC: 3.6.1.55,3.6.1.56; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NUDT1, MTH1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ALPHA-BETA-ALPHA SANDWICH, HYDROLASE, DNA DAMAGE, DNA REPAIR, DNA KEYWDS 2 REPLICATION EXPDTA X-RAY DIFFRACTION AUTHOR T.NAKAMURA,S.WAZ,K.HIRATA,Y.NAKABEPPU,Y.YAMAGATA REVDAT 2 27-MAR-24 6ILI 1 REMARK REVDAT 1 07-NOV-18 6ILI 0 JRNL AUTH S.WAZ,T.NAKAMURA,K.HIRATA,Y.KOGA-OGAWA,M.CHIRIFU,T.ARIMORI, JRNL AUTH 2 T.TAMADA,S.IKEMIZU,Y.NAKABEPPU,Y.YAMAGATA JRNL TITL STRUCTURAL AND KINETIC STUDIES OF THE HUMAN NUDIX HYDROLASE JRNL TITL 2 MTH1 REVEAL THE MECHANISM FOR ITS BROAD SUBSTRATE JRNL TITL 3 SPECIFICITY JRNL REF J. BIOL. CHEM. V. 292 2785 2017 JRNL REFN ESSN 1083-351X JRNL PMID 28035004 JRNL DOI 10.1074/JBC.M116.749713 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.KOGA,M.INAZATO,T.NAKAMURA,C.HASHIKAWA,M.CHIRIFU,A.MICHI, REMARK 1 AUTH 2 T.YAMASHITA,S.TOMA,A.KUNIYASU,S.IKEMIZU,Y.NAKABEPPU, REMARK 1 AUTH 3 Y.YAMAGATA REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY ANALYSIS OF HUMAN MTH1 REMARK 1 TITL 2 WITH A HOMOGENEOUS N-TERMINUS. REMARK 1 REF ACTA CRYSTALLOGR. SECT. F V. 69 45 2013 REMARK 1 REF 2 STRUCT. BIOL. CRYST. COMMUN. REMARK 1 REFN ESSN 1744-3091 REMARK 1 PMID 23295485 REMARK 1 DOI 10.1107/S1744309112048002 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 48102 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 2433 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 37.4256 - 3.7239 0.97 2853 150 0.1659 0.1758 REMARK 3 2 3.7239 - 2.9561 1.00 2799 118 0.1514 0.1757 REMARK 3 3 2.9561 - 2.5826 1.00 2747 142 0.1827 0.2260 REMARK 3 4 2.5826 - 2.3465 1.00 2715 144 0.1845 0.2002 REMARK 3 5 2.3465 - 2.1783 1.00 2701 167 0.1789 0.2176 REMARK 3 6 2.1783 - 2.0499 1.00 2662 163 0.1725 0.2139 REMARK 3 7 2.0499 - 1.9472 1.00 2700 144 0.1751 0.1960 REMARK 3 8 1.9472 - 1.8625 1.00 2693 148 0.1794 0.2144 REMARK 3 9 1.8625 - 1.7908 1.00 2662 155 0.1881 0.2035 REMARK 3 10 1.7908 - 1.7290 1.00 2674 126 0.1839 0.2449 REMARK 3 11 1.7290 - 1.6749 1.00 2686 131 0.1820 0.2085 REMARK 3 12 1.6749 - 1.6271 0.99 2678 124 0.1893 0.2384 REMARK 3 13 1.6271 - 1.5842 0.99 2623 157 0.1791 0.2457 REMARK 3 14 1.5842 - 1.5456 0.99 2674 139 0.1901 0.2096 REMARK 3 15 1.5456 - 1.5104 0.99 2656 137 0.1893 0.2199 REMARK 3 16 1.5104 - 1.4783 0.99 2608 151 0.2003 0.2745 REMARK 3 17 1.4783 - 1.4487 0.95 2538 137 0.2160 0.2817 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.120 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 : 0.013 2878 REMARK 3 ANGLE : 1.466 3928 REMARK 3 CHIRALITY : 0.102 406 REMARK 3 PLANARITY : 0.010 504 REMARK 3 DIHEDRAL : 17.077 1092 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 20 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.0920 -0.6462 -15.8387 REMARK 3 T TENSOR REMARK 3 T11: 0.1108 T22: 0.1159 REMARK 3 T33: 0.0906 T12: 0.0155 REMARK 3 T13: 0.0112 T23: 0.0145 REMARK 3 L TENSOR REMARK 3 L11: 2.2705 L22: 1.6145 REMARK 3 L33: 1.2608 L12: -1.0618 REMARK 3 L13: 0.7591 L23: 0.5238 REMARK 3 S TENSOR REMARK 3 S11: -0.0129 S12: 0.1592 S13: 0.2091 REMARK 3 S21: -0.2917 S22: -0.0443 S23: 0.0651 REMARK 3 S31: 0.0506 S32: 0.0495 S33: 0.1087 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 12 THROUGH 34 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.3353 -17.1632 -16.2127 REMARK 3 T TENSOR REMARK 3 T11: 0.1923 T22: 0.1329 REMARK 3 T33: 0.1329 T12: 0.0317 REMARK 3 T13: 0.0137 T23: 0.0052 REMARK 3 L TENSOR REMARK 3 L11: 2.9972 L22: 2.1982 REMARK 3 L33: 3.8183 L12: 1.2354 REMARK 3 L13: 0.0051 L23: -0.2440 REMARK 3 S TENSOR REMARK 3 S11: -0.1887 S12: -0.0749 S13: 0.2507 REMARK 3 S21: 0.1135 S22: 0.1764 S23: 0.3731 REMARK 3 S31: -0.3937 S32: -0.4647 S33: 0.0568 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 35 THROUGH 57 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.5175 -8.0757 -5.4106 REMARK 3 T TENSOR REMARK 3 T11: 0.2419 T22: 0.1353 REMARK 3 T33: 0.0979 T12: 0.0118 REMARK 3 T13: 0.0180 T23: -0.0050 REMARK 3 L TENSOR REMARK 3 L11: 3.4413 L22: 6.5400 REMARK 3 L33: 0.8430 L12: -0.0800 REMARK 3 L13: -0.5337 L23: -0.2904 REMARK 3 S TENSOR REMARK 3 S11: 0.0136 S12: -0.2495 S13: 0.0413 REMARK 3 S21: 0.9144 S22: 0.0196 S23: 0.2364 REMARK 3 S31: -0.2727 S32: 0.0227 S33: 0.0103 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 58 THROUGH 74 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.3551 -9.9658 -13.8194 REMARK 3 T TENSOR REMARK 3 T11: 0.2052 T22: 0.1835 REMARK 3 T33: 0.1352 T12: 0.0254 REMARK 3 T13: 0.0027 T23: 0.0062 REMARK 3 L TENSOR REMARK 3 L11: 1.6127 L22: 2.4698 REMARK 3 L33: 1.3930 L12: 0.8773 REMARK 3 L13: -1.1764 L23: -1.8862 REMARK 3 S TENSOR REMARK 3 S11: 0.1203 S12: -0.2502 S13: -0.1853 REMARK 3 S21: 0.2103 S22: -0.3813 S23: -0.1076 REMARK 3 S31: 0.0175 S32: 0.4323 S33: 0.2603 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 75 THROUGH 88 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.338 -2.992 -17.834 REMARK 3 T TENSOR REMARK 3 T11: 0.1528 T22: 0.1299 REMARK 3 T33: 0.1202 T12: 0.0219 REMARK 3 T13: 0.0059 T23: -0.0095 REMARK 3 L TENSOR REMARK 3 L11: 1.7130 L22: 2.5642 REMARK 3 L33: 1.9899 L12: -0.6068 REMARK 3 L13: 1.1500 L23: -2.0992 REMARK 3 S TENSOR REMARK 3 S11: 0.0612 S12: 0.0057 S13: -0.0347 REMARK 3 S21: 0.0709 S22: -0.1940 S23: -0.0858 REMARK 3 S31: 0.0828 S32: 0.0377 S33: 0.0762 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 89 THROUGH 100 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.758 -20.9644 -5.4514 REMARK 3 T TENSOR REMARK 3 T11: 0.3473 T22: 0.1559 REMARK 3 T33: 0.1307 T12: 0.0015 REMARK 3 T13: -0.0139 T23: -0.0202 REMARK 3 L TENSOR REMARK 3 L11: 5.5459 L22: 6.8586 REMARK 3 L33: 3.4227 L12: -3.0673 REMARK 3 L13: 0.6453 L23: -1.6198 REMARK 3 S TENSOR REMARK 3 S11: -0.1279 S12: -0.9084 S13: 0.6209 REMARK 3 S21: 0.4483 S22: 0.1196 S23: -0.1943 REMARK 3 S31: -0.6313 S32: -0.0219 S33: 0.2044 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 101 THROUGH 117 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.0382 -21.2608 -19.9861 REMARK 3 T TENSOR REMARK 3 T11: 0.1373 T22: 0.1040 REMARK 3 T33: 0.1115 T12: 0.0079 REMARK 3 T13: 0.0126 T23: 0.0109 REMARK 3 L TENSOR REMARK 3 L11: 1.1627 L22: 3.2837 REMARK 3 L33: 1.8144 L12: -1.0634 REMARK 3 L13: 0.3839 L23: -0.7660 REMARK 3 S TENSOR REMARK 3 S11: -0.0414 S12: -0.0255 S13: 0.0743 REMARK 3 S21: 0.0807 S22: 0.0874 S23: 0.0635 REMARK 3 S31: -0.1417 S32: -0.2285 S33: -0.0561 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 118 THROUGH 128 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.7379 -15.3819 -24.8179 REMARK 3 T TENSOR REMARK 3 T11: 0.2040 T22: 0.1178 REMARK 3 T33: 0.1630 T12: -0.0277 REMARK 3 T13: 0.0190 T23: 0.0127 REMARK 3 L TENSOR REMARK 3 L11: 3.2261 L22: 2.5716 REMARK 3 L33: 1.6401 L12: -1.6606 REMARK 3 L13: 0.1594 L23: 0.2367 REMARK 3 S TENSOR REMARK 3 S11: 0.0573 S12: -0.1384 S13: -0.2055 REMARK 3 S21: 0.1193 S22: 0.0689 S23: 0.1847 REMARK 3 S31: 0.1404 S32: -0.1780 S33: -0.1515 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 129 THROUGH 156 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.8451 -7.5664 -26.7545 REMARK 3 T TENSOR REMARK 3 T11: 0.1138 T22: 0.0816 REMARK 3 T33: 0.0808 T12: 0.0022 REMARK 3 T13: 0.0201 T23: -0.0013 REMARK 3 L TENSOR REMARK 3 L11: 4.2023 L22: 3.8304 REMARK 3 L33: 2.2452 L12: -2.6835 REMARK 3 L13: 1.5850 L23: -0.7525 REMARK 3 S TENSOR REMARK 3 S11: -0.1420 S12: -0.1334 S13: 0.0664 REMARK 3 S21: 0.2170 S22: 0.1339 S23: -0.1085 REMARK 3 S31: 0.0660 S32: 0.0834 S33: 0.0277 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.4784 8.0883 -14.2159 REMARK 3 T TENSOR REMARK 3 T11: 0.1052 T22: 0.1350 REMARK 3 T33: 0.0990 T12: 0.0034 REMARK 3 T13: -0.0139 T23: 0.0022 REMARK 3 L TENSOR REMARK 3 L11: 8.2533 L22: 0.5979 REMARK 3 L33: 1.2339 L12: 0.2638 REMARK 3 L13: -2.3171 L23: 0.2664 REMARK 3 S TENSOR REMARK 3 S11: -0.0235 S12: 0.0125 S13: 0.0978 REMARK 3 S21: -0.0029 S22: 0.0135 S23: 0.0625 REMARK 3 S31: 0.0433 S32: -0.1367 S33: -0.0201 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 12 THROUGH 23 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.7725 13.4069 -16.0279 REMARK 3 T TENSOR REMARK 3 T11: 0.0777 T22: 0.1152 REMARK 3 T33: 0.0793 T12: 0.0065 REMARK 3 T13: 0.0226 T23: 0.0266 REMARK 3 L TENSOR REMARK 3 L11: 2.5738 L22: 6.9499 REMARK 3 L33: 2.9023 L12: -1.3466 REMARK 3 L13: -0.5026 L23: 0.9106 REMARK 3 S TENSOR REMARK 3 S11: 0.1056 S12: 0.1888 S13: -0.0382 REMARK 3 S21: -0.1066 S22: -0.1035 S23: 0.1784 REMARK 3 S31: -0.0896 S32: -0.1875 S33: -0.0319 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 24 THROUGH 33 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.0011 23.0248 -13.9764 REMARK 3 T TENSOR REMARK 3 T11: 0.3844 T22: 0.5846 REMARK 3 T33: 0.2419 T12: 0.2112 REMARK 3 T13: 0.0183 T23: 0.1128 REMARK 3 L TENSOR REMARK 3 L11: 0.6090 L22: 0.8636 REMARK 3 L33: 5.1043 L12: -0.1032 REMARK 3 L13: -0.9099 L23: -0.3649 REMARK 3 S TENSOR REMARK 3 S11: 0.3651 S12: 1.0419 S13: -0.1104 REMARK 3 S21: -0.7625 S22: 0.1475 S23: 0.4991 REMARK 3 S31: -0.9344 S32: -2.4184 S33: -0.2905 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 34 THROUGH 44 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.2797 9.2826 -24.0188 REMARK 3 T TENSOR REMARK 3 T11: 0.1415 T22: 0.3307 REMARK 3 T33: 0.1695 T12: -0.0708 REMARK 3 T13: -0.0139 T23: 0.0314 REMARK 3 L TENSOR REMARK 3 L11: 5.6299 L22: 7.0262 REMARK 3 L33: 4.3467 L12: 1.7233 REMARK 3 L13: 2.0470 L23: 3.0052 REMARK 3 S TENSOR REMARK 3 S11: -0.3270 S12: 0.9489 S13: 0.0406 REMARK 3 S21: -0.5535 S22: 0.2409 S23: 0.4953 REMARK 3 S31: 0.0468 S32: -0.4096 S33: 0.1313 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 45 THROUGH 59 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.6942 9.7046 -26.0708 REMARK 3 T TENSOR REMARK 3 T11: 0.1546 T22: 0.4424 REMARK 3 T33: 0.1526 T12: -0.0566 REMARK 3 T13: 0.0389 T23: 0.0012 REMARK 3 L TENSOR REMARK 3 L11: 6.6549 L22: 4.0384 REMARK 3 L33: 0.5422 L12: 3.1222 REMARK 3 L13: 0.4799 L23: -0.9483 REMARK 3 S TENSOR REMARK 3 S11: -0.6888 S12: 1.2544 S13: 0.8949 REMARK 3 S21: -0.4104 S22: 0.3322 S23: 0.1034 REMARK 3 S31: 0.3368 S32: -0.7059 S33: -0.2245 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 60 THROUGH 88 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.8220 6.6485 -14.4846 REMARK 3 T TENSOR REMARK 3 T11: 0.1080 T22: 0.1486 REMARK 3 T33: 0.0850 T12: 0.0115 REMARK 3 T13: -0.0253 T23: -0.0003 REMARK 3 L TENSOR REMARK 3 L11: 3.0102 L22: 2.7620 REMARK 3 L33: 1.2453 L12: -0.6827 REMARK 3 L13: -1.5027 L23: 0.3828 REMARK 3 S TENSOR REMARK 3 S11: -0.1900 S12: 0.0501 S13: -0.1638 REMARK 3 S21: -0.0694 S22: 0.1089 S23: -0.0202 REMARK 3 S31: 0.0049 S32: 0.0755 S33: 0.0808 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 89 THROUGH 100 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.5683 15.2848 -25.4009 REMARK 3 T TENSOR REMARK 3 T11: 0.1994 T22: 0.2600 REMARK 3 T33: 0.1215 T12: 0.0923 REMARK 3 T13: 0.0279 T23: 0.0761 REMARK 3 L TENSOR REMARK 3 L11: 4.7012 L22: 5.8464 REMARK 3 L33: 2.5926 L12: -0.3891 REMARK 3 L13: -0.6907 L23: 0.7370 REMARK 3 S TENSOR REMARK 3 S11: -0.3196 S12: 0.1718 S13: 0.0242 REMARK 3 S21: 0.1082 S22: 0.5635 S23: 0.2427 REMARK 3 S31: -0.2790 S32: -0.7429 S33: 0.1031 REMARK 3 TLS GROUP : 17 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 101 THROUGH 117 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.6396 17.0506 -11.3778 REMARK 3 T TENSOR REMARK 3 T11: 0.1230 T22: 0.0975 REMARK 3 T33: 0.1135 T12: 0.0124 REMARK 3 T13: 0.0074 T23: 0.0043 REMARK 3 L TENSOR REMARK 3 L11: 5.1692 L22: 1.9667 REMARK 3 L33: 2.7955 L12: -1.3476 REMARK 3 L13: -0.4392 L23: -0.1899 REMARK 3 S TENSOR REMARK 3 S11: 0.0968 S12: -0.0613 S13: 0.1464 REMARK 3 S21: -0.0586 S22: -0.0653 S23: 0.0401 REMARK 3 S31: -0.2367 S32: -0.0996 S33: 0.0024 REMARK 3 TLS GROUP : 18 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 118 THROUGH 128 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.9945 7.8325 -5.9609 REMARK 3 T TENSOR REMARK 3 T11: 0.1208 T22: 0.3052 REMARK 3 T33: 0.1551 T12: -0.1023 REMARK 3 T13: -0.0371 T23: 0.0871 REMARK 3 L TENSOR REMARK 3 L11: 2.5037 L22: 3.0020 REMARK 3 L33: 1.6821 L12: -1.7383 REMARK 3 L13: -0.0686 L23: -1.7200 REMARK 3 S TENSOR REMARK 3 S11: 0.0189 S12: -0.0541 S13: 0.0735 REMARK 3 S21: 0.3380 S22: -0.0836 S23: -0.1878 REMARK 3 S31: -0.4241 S32: 0.2731 S33: 0.0200 REMARK 3 TLS GROUP : 19 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 129 THROUGH 140 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.6696 5.1096 -5.5132 REMARK 3 T TENSOR REMARK 3 T11: 0.0742 T22: 0.1530 REMARK 3 T33: 0.0796 T12: 0.0010 REMARK 3 T13: -0.0065 T23: 0.0458 REMARK 3 L TENSOR REMARK 3 L11: 6.0207 L22: 4.4566 REMARK 3 L33: 3.0942 L12: -3.3000 REMARK 3 L13: -2.5318 L23: 1.7052 REMARK 3 S TENSOR REMARK 3 S11: 0.1581 S12: 0.2636 S13: -0.1133 REMARK 3 S21: -0.0509 S22: -0.3129 S23: -0.0731 REMARK 3 S31: -0.2476 S32: 0.1280 S33: 0.0236 REMARK 3 TLS GROUP : 20 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 141 THROUGH 156 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.6834 5.5568 -2.9675 REMARK 3 T TENSOR REMARK 3 T11: 0.1571 T22: 0.1470 REMARK 3 T33: 0.0794 T12: 0.0176 REMARK 3 T13: -0.0182 T23: 0.0226 REMARK 3 L TENSOR REMARK 3 L11: 4.2214 L22: 2.8757 REMARK 3 L33: 2.4628 L12: -2.2152 REMARK 3 L13: -1.1999 L23: 0.4133 REMARK 3 S TENSOR REMARK 3 S11: 0.0706 S12: 0.1414 S13: -0.1898 REMARK 3 S21: -0.2715 S22: -0.1685 S23: 0.3431 REMARK 3 S31: -0.0496 S32: 0.1855 S33: 0.1071 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 6ILI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1300009331. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-SEP-15 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 : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48166 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 46.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.41000 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: FOURIER SYNTHESIS 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 (%): 33.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CITRATE, CACODYLATE, NACL, PH REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 23.03550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.51600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.56600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.51600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.03550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.56600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 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 92 32.29 -150.90 REMARK 500 GLN A 92 27.93 -154.23 REMARK 500 PHE B 27 96.25 -67.26 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 8DG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8DG B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GHM RELATED DB: PDB DBREF 6ILI A 1 156 UNP P36639 8ODP_HUMAN 42 197 DBREF 6ILI B 1 156 UNP P36639 8ODP_HUMAN 42 197 SEQADV 6ILI LYS A 2 UNP P36639 GLY 43 ENGINEERED MUTATION SEQADV 6ILI ASN A 120 UNP P36639 ASP 161 ENGINEERED MUTATION SEQADV 6ILI LYS B 2 UNP P36639 GLY 43 ENGINEERED MUTATION SEQADV 6ILI ASN B 120 UNP P36639 ASP 161 ENGINEERED MUTATION SEQRES 1 A 156 MET LYS ALA SER ARG LEU TYR THR LEU VAL LEU VAL LEU SEQRES 2 A 156 GLN PRO GLN ARG VAL LEU LEU GLY MET LYS LYS ARG GLY SEQRES 3 A 156 PHE GLY ALA GLY ARG TRP ASN GLY PHE GLY GLY LYS VAL SEQRES 4 A 156 GLN GLU GLY GLU THR ILE GLU ASP GLY ALA ARG ARG GLU SEQRES 5 A 156 LEU GLN GLU GLU SER GLY LEU THR VAL ASP ALA LEU HIS SEQRES 6 A 156 LYS VAL GLY GLN ILE VAL PHE GLU PHE VAL GLY GLU PRO SEQRES 7 A 156 GLU LEU MET ASP VAL HIS VAL PHE CYS THR ASP SER ILE SEQRES 8 A 156 GLN GLY THR PRO VAL GLU SER ASP GLU MET ARG PRO CYS SEQRES 9 A 156 TRP PHE GLN LEU ASP GLN ILE PRO PHE LYS ASP MET TRP SEQRES 10 A 156 PRO ASP ASN SER TYR TRP PHE PRO LEU LEU LEU GLN LYS SEQRES 11 A 156 LYS LYS PHE HIS GLY TYR PHE LYS PHE GLN GLY GLN ASP SEQRES 12 A 156 THR ILE LEU ASP TYR THR LEU ARG GLU VAL ASP THR VAL SEQRES 1 B 156 MET LYS ALA SER ARG LEU TYR THR LEU VAL LEU VAL LEU SEQRES 2 B 156 GLN PRO GLN ARG VAL LEU LEU GLY MET LYS LYS ARG GLY SEQRES 3 B 156 PHE GLY ALA GLY ARG TRP ASN GLY PHE GLY GLY LYS VAL SEQRES 4 B 156 GLN GLU GLY GLU THR ILE GLU ASP GLY ALA ARG ARG GLU SEQRES 5 B 156 LEU GLN GLU GLU SER GLY LEU THR VAL ASP ALA LEU HIS SEQRES 6 B 156 LYS VAL GLY GLN ILE VAL PHE GLU PHE VAL GLY GLU PRO SEQRES 7 B 156 GLU LEU MET ASP VAL HIS VAL PHE CYS THR ASP SER ILE SEQRES 8 B 156 GLN GLY THR PRO VAL GLU SER ASP GLU MET ARG PRO CYS SEQRES 9 B 156 TRP PHE GLN LEU ASP GLN ILE PRO PHE LYS ASP MET TRP SEQRES 10 B 156 PRO ASP ASN SER TYR TRP PHE PRO LEU LEU LEU GLN LYS SEQRES 11 B 156 LYS LYS PHE HIS GLY TYR PHE LYS PHE GLN GLY GLN ASP SEQRES 12 B 156 THR ILE LEU ASP TYR THR LEU ARG GLU VAL ASP THR VAL HET 8DG A 201 32 HET 8DG B 201 32 HETNAM 8DG 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE FORMUL 3 8DG 2(C10 H16 N5 O14 P3) FORMUL 5 HOH *324(H2 O) HELIX 1 AA1 THR A 44 GLY A 58 1 15 HELIX 2 AA2 PRO A 112 MET A 116 5 5 HELIX 3 AA3 TRP A 117 PRO A 118 5 2 HELIX 4 AA4 ASP A 119 GLN A 129 1 11 HELIX 5 AA5 THR B 44 GLY B 58 1 15 HELIX 6 AA6 PRO B 112 MET B 116 5 5 HELIX 7 AA7 TRP B 117 PRO B 118 5 2 HELIX 8 AA8 ASP B 119 GLN B 129 1 11 SHEET 1 AA1 4 TRP A 32 ASN A 33 0 SHEET 2 AA1 4 ARG A 17 LYS A 23 -1 N GLY A 21 O ASN A 33 SHEET 3 AA1 4 SER A 4 LEU A 13 -1 N VAL A 12 O LEU A 19 SHEET 4 AA1 4 MET A 101 GLN A 107 0 SHEET 1 AA2 7 PHE A 35 LYS A 38 0 SHEET 2 AA2 7 SER A 4 LEU A 13 -1 N VAL A 10 O PHE A 35 SHEET 3 AA2 7 ARG A 17 LYS A 23 -1 O LEU A 19 N VAL A 12 SHEET 4 AA2 7 LEU A 80 THR A 88 0 SHEET 5 AA2 7 LEU A 64 PHE A 74 -1 N ILE A 70 O VAL A 83 SHEET 6 AA2 7 LYS A 132 GLN A 140 1 O PHE A 139 N GLU A 73 SHEET 7 AA2 7 THR A 144 VAL A 153 -1 O ASP A 147 N LYS A 138 SHEET 1 AA3 3 TRP B 32 ASN B 33 0 SHEET 2 AA3 3 ARG B 17 LYS B 23 -1 N GLY B 21 O ASN B 33 SHEET 3 AA3 3 MET B 101 GLN B 107 -1 O CYS B 104 N LEU B 20 SHEET 1 AA4 7 TRP B 32 ASN B 33 0 SHEET 2 AA4 7 ARG B 17 LYS B 23 -1 N GLY B 21 O ASN B 33 SHEET 3 AA4 7 SER B 4 LEU B 13 -1 N VAL B 12 O LEU B 19 SHEET 4 AA4 7 LEU B 80 GLN B 92 1 O PHE B 86 N LEU B 9 SHEET 5 AA4 7 THR B 60 PHE B 74 -1 N ALA B 63 O ASP B 89 SHEET 6 AA4 7 LYS B 132 GLN B 140 1 O PHE B 137 N VAL B 71 SHEET 7 AA4 7 THR B 144 VAL B 153 -1 O ASP B 147 N LYS B 138 SITE 1 AC1 15 TYR A 7 ASN A 33 GLY A 37 LYS A 38 SITE 2 AC1 15 PHE A 72 MET A 81 TRP A 117 ASP A 119 SITE 3 AC1 15 ASN A 120 PHE A 139 HOH A 304 HOH A 361 SITE 4 AC1 15 HOH A 408 HOH A 424 LYS B 130 SITE 1 AC2 12 TYR B 7 LYS B 23 ASN B 33 LYS B 38 SITE 2 AC2 12 PHE B 72 MET B 81 TRP B 117 ASP B 119 SITE 3 AC2 12 ASN B 120 PHE B 139 HOH B 376 HOH B 385 CRYST1 46.071 47.132 123.032 90.00 90.00 90.00 P 21 21 21 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 0.021706 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021217 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008128 0.00000