HEADER HYDROLASE 20-JUN-16 5GHM TITLE CRYSTAL STRUCTURE OF HUMAN MTH1(G2K/D120N MUTANT) IN COMPLEX WITH 8- TITLE 2 OXO-DGTP AT PH 7.0 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 42-197; COMPND 5 SYNONYM: MUTT HOMOLOGUE-1,2-HYDROXY-DATP DIPHOSPHATASE,8-OXO-DGTPASE, COMPND 6 NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 1,NUDIX MOTIF 1; COMPND 7 EC: 3.6.1.55,3.6.1.56; COMPND 8 ENGINEERED: YES; COMPND 9 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; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) 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 5 20-MAR-24 5GHM 1 LINK REVDAT 4 07-NOV-18 5GHM 1 TITLE REMARK REVDAT 3 01-MAR-17 5GHM 1 JRNL REVDAT 2 11-JAN-17 5GHM 1 JRNL REVDAT 1 04-JAN-17 5GHM 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. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 44286 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 2238 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 37.8122 - 3.7731 0.98 2793 133 0.1593 0.1572 REMARK 3 2 3.7731 - 2.9952 1.00 2717 129 0.1463 0.1517 REMARK 3 3 2.9952 - 2.6167 1.00 2675 152 0.1859 0.2238 REMARK 3 4 2.6167 - 2.3775 1.00 2643 136 0.1826 0.1978 REMARK 3 5 2.3775 - 2.2071 1.00 2627 138 0.1742 0.2120 REMARK 3 6 2.2071 - 2.0770 1.00 2618 145 0.1754 0.2005 REMARK 3 7 2.0770 - 1.9730 1.00 2651 139 0.1736 0.2156 REMARK 3 8 1.9730 - 1.8871 1.00 2585 149 0.1729 0.1878 REMARK 3 9 1.8871 - 1.8145 1.00 2631 136 0.1843 0.2109 REMARK 3 10 1.8145 - 1.7518 1.00 2597 132 0.1895 0.2399 REMARK 3 11 1.7518 - 1.6971 1.00 2586 145 0.1901 0.2316 REMARK 3 12 1.6971 - 1.6486 1.00 2623 138 0.1948 0.2374 REMARK 3 13 1.6486 - 1.6052 1.00 2594 155 0.1884 0.2322 REMARK 3 14 1.6052 - 1.5660 1.00 2608 133 0.1910 0.2198 REMARK 3 15 1.5660 - 1.5304 1.00 2577 148 0.1934 0.2372 REMARK 3 16 1.5304 - 1.4978 0.97 2523 130 0.2017 0.2624 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.280 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 : 0.006 2976 REMARK 3 ANGLE : 0.927 4085 REMARK 3 CHIRALITY : 0.078 415 REMARK 3 PLANARITY : 0.006 536 REMARK 3 DIHEDRAL : 16.680 1134 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 18 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.9399 -3.8045 -15.6076 REMARK 3 T TENSOR REMARK 3 T11: 0.1300 T22: 0.0901 REMARK 3 T33: 0.0687 T12: -0.0193 REMARK 3 T13: 0.0156 T23: 0.0063 REMARK 3 L TENSOR REMARK 3 L11: 1.7274 L22: 4.5445 REMARK 3 L33: 1.0348 L12: -2.4622 REMARK 3 L13: 0.9042 L23: -0.6351 REMARK 3 S TENSOR REMARK 3 S11: 0.0724 S12: 0.0884 S13: 0.0279 REMARK 3 S21: 0.0492 S22: -0.2447 S23: 0.0449 REMARK 3 S31: -0.0362 S32: 0.0424 S33: 0.1336 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 13 THROUGH 33 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.9925 -18.3945 -16.4305 REMARK 3 T TENSOR REMARK 3 T11: 0.1305 T22: 0.0952 REMARK 3 T33: 0.1322 T12: 0.0035 REMARK 3 T13: 0.0130 T23: 0.0310 REMARK 3 L TENSOR REMARK 3 L11: 4.1161 L22: 4.7859 REMARK 3 L33: 5.1885 L12: 0.3307 REMARK 3 L13: -0.2576 L23: 0.3880 REMARK 3 S TENSOR REMARK 3 S11: -0.2179 S12: -0.0858 S13: 0.4650 REMARK 3 S21: 0.0947 S22: 0.2284 S23: 0.3962 REMARK 3 S31: -0.4852 S32: -0.5244 S33: 0.0932 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 34 THROUGH 44 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.8422 -4.6006 -6.9123 REMARK 3 T TENSOR REMARK 3 T11: 0.2744 T22: 0.0757 REMARK 3 T33: 0.1278 T12: -0.0347 REMARK 3 T13: -0.0094 T23: -0.0251 REMARK 3 L TENSOR REMARK 3 L11: 4.7055 L22: 2.0150 REMARK 3 L33: 1.6485 L12: -0.4422 REMARK 3 L13: -0.1821 L23: 0.4885 REMARK 3 S TENSOR REMARK 3 S11: 0.1417 S12: -0.2936 S13: 0.3593 REMARK 3 S21: 0.9655 S22: -0.0929 S23: -0.1658 REMARK 3 S31: -0.0627 S32: -0.1150 S33: 0.0162 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 45 THROUGH 57 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.0945 -10.9864 -5.0438 REMARK 3 T TENSOR REMARK 3 T11: 0.2743 T22: 0.1124 REMARK 3 T33: 0.1759 T12: -0.0001 REMARK 3 T13: 0.0261 T23: 0.0363 REMARK 3 L TENSOR REMARK 3 L11: 4.0965 L22: 3.5420 REMARK 3 L33: 4.8958 L12: 2.9786 REMARK 3 L13: -2.3180 L23: -1.3858 REMARK 3 S TENSOR REMARK 3 S11: 0.1169 S12: -0.1822 S13: 0.0341 REMARK 3 S21: 0.7834 S22: -0.1206 S23: 0.4154 REMARK 3 S31: -0.6896 S32: -0.1138 S33: -0.0822 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 58 THROUGH 88 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.4466 -8.5039 -15.2840 REMARK 3 T TENSOR REMARK 3 T11: 0.1313 T22: 0.0950 REMARK 3 T33: 0.0884 T12: -0.0265 REMARK 3 T13: -0.0080 T23: -0.0038 REMARK 3 L TENSOR REMARK 3 L11: 1.7154 L22: 3.8360 REMARK 3 L33: 2.2010 L12: -0.4229 REMARK 3 L13: 0.3769 L23: -2.2060 REMARK 3 S TENSOR REMARK 3 S11: 0.1088 S12: -0.1014 S13: -0.0679 REMARK 3 S21: 0.1836 S22: -0.2050 S23: -0.1478 REMARK 3 S31: 0.0446 S32: 0.0333 S33: 0.1232 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 89 THROUGH 100 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.7923 -20.3448 -5.9026 REMARK 3 T TENSOR REMARK 3 T11: 0.2470 T22: 0.1970 REMARK 3 T33: 0.1324 T12: -0.0138 REMARK 3 T13: 0.0525 T23: -0.0120 REMARK 3 L TENSOR REMARK 3 L11: 2.1713 L22: 7.0272 REMARK 3 L33: 3.4516 L12: -1.6425 REMARK 3 L13: -2.1496 L23: 0.1322 REMARK 3 S TENSOR REMARK 3 S11: 0.4380 S12: -0.7682 S13: 0.2226 REMARK 3 S21: 0.1800 S22: -0.0822 S23: 0.2724 REMARK 3 S31: -0.2991 S32: 0.1062 S33: -0.1351 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 101 THROUGH 117 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.4091 -21.5358 -19.5606 REMARK 3 T TENSOR REMARK 3 T11: 0.0746 T22: 0.0750 REMARK 3 T33: 0.0897 T12: 0.0105 REMARK 3 T13: 0.0053 T23: 0.0105 REMARK 3 L TENSOR REMARK 3 L11: 2.2280 L22: 6.0560 REMARK 3 L33: 1.9266 L12: -1.5649 REMARK 3 L13: 0.0395 L23: 0.4571 REMARK 3 S TENSOR REMARK 3 S11: -0.0339 S12: -0.0212 S13: 0.0929 REMARK 3 S21: -0.0340 S22: 0.0371 S23: 0.1237 REMARK 3 S31: -0.0960 S32: -0.2469 S33: -0.0280 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 118 THROUGH 156 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.6316 -10.4065 -26.2446 REMARK 3 T TENSOR REMARK 3 T11: 0.1275 T22: 0.0610 REMARK 3 T33: 0.0601 T12: -0.0065 REMARK 3 T13: 0.0284 T23: -0.0100 REMARK 3 L TENSOR REMARK 3 L11: 3.9966 L22: 4.5307 REMARK 3 L33: 2.8307 L12: -2.9929 REMARK 3 L13: 1.5894 L23: -1.6817 REMARK 3 S TENSOR REMARK 3 S11: -0.0869 S12: -0.0727 S13: -0.0402 REMARK 3 S21: 0.2436 S22: 0.0236 S23: -0.0302 REMARK 3 S31: 0.1803 S32: 0.0590 S33: 0.0704 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.6088 7.9630 -14.7453 REMARK 3 T TENSOR REMARK 3 T11: 0.0678 T22: 0.0902 REMARK 3 T33: 0.0830 T12: -0.0207 REMARK 3 T13: -0.0047 T23: 0.0010 REMARK 3 L TENSOR REMARK 3 L11: 4.6102 L22: 0.9995 REMARK 3 L33: 2.0748 L12: -0.0631 REMARK 3 L13: -2.3368 L23: 0.2609 REMARK 3 S TENSOR REMARK 3 S11: -0.1298 S12: 0.3026 S13: 0.0625 REMARK 3 S21: -0.0099 S22: 0.0565 S23: 0.1368 REMARK 3 S31: 0.0945 S32: -0.2583 S33: 0.0581 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 13 THROUGH 23 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.4320 13.9577 -15.5870 REMARK 3 T TENSOR REMARK 3 T11: 0.0371 T22: 0.1153 REMARK 3 T33: 0.1140 T12: -0.0202 REMARK 3 T13: 0.0066 T23: 0.0269 REMARK 3 L TENSOR REMARK 3 L11: 2.6991 L22: 5.9928 REMARK 3 L33: 4.9189 L12: -2.3738 REMARK 3 L13: -2.2754 L23: 1.1078 REMARK 3 S TENSOR REMARK 3 S11: 0.1655 S12: -0.0328 S13: -0.0260 REMARK 3 S21: -0.1645 S22: -0.1751 S23: -0.0592 REMARK 3 S31: -0.1375 S32: -0.0487 S33: -0.0257 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 24 THROUGH 34 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.6793 22.0414 -14.2344 REMARK 3 T TENSOR REMARK 3 T11: 0.2036 T22: 0.3484 REMARK 3 T33: 0.1895 T12: 0.0717 REMARK 3 T13: 0.0567 T23: 0.0635 REMARK 3 L TENSOR REMARK 3 L11: 5.7140 L22: 2.8797 REMARK 3 L33: 1.1334 L12: -0.8760 REMARK 3 L13: 1.2762 L23: -0.0510 REMARK 3 S TENSOR REMARK 3 S11: 0.3024 S12: 0.6126 S13: 0.4811 REMARK 3 S21: -0.1074 S22: 0.0102 S23: 0.2629 REMARK 3 S31: -0.4498 S32: -1.0577 S33: -0.2308 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 35 THROUGH 57 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.9992 9.4553 -25.6882 REMARK 3 T TENSOR REMARK 3 T11: 0.2043 T22: 0.3907 REMARK 3 T33: 0.1122 T12: -0.1419 REMARK 3 T13: -0.0025 T23: 0.0035 REMARK 3 L TENSOR REMARK 3 L11: 5.8810 L22: 3.5992 REMARK 3 L33: 0.3005 L12: 1.1772 REMARK 3 L13: 0.1529 L23: 0.6782 REMARK 3 S TENSOR REMARK 3 S11: -0.3638 S12: 1.3596 S13: 0.3669 REMARK 3 S21: -0.7201 S22: 0.3556 S23: 0.0627 REMARK 3 S31: 0.3874 S32: -0.6148 S33: 0.0541 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 58 THROUGH 74 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.9614 5.7404 -16.5172 REMARK 3 T TENSOR REMARK 3 T11: 0.1215 T22: 0.1637 REMARK 3 T33: 0.1204 T12: -0.0271 REMARK 3 T13: 0.0008 T23: -0.0214 REMARK 3 L TENSOR REMARK 3 L11: 1.6617 L22: 1.6247 REMARK 3 L33: 3.7997 L12: 1.3439 REMARK 3 L13: -2.0010 L23: -1.2683 REMARK 3 S TENSOR REMARK 3 S11: -0.3818 S12: 0.1878 S13: -0.1993 REMARK 3 S21: -0.2825 S22: 0.1685 S23: -0.1785 REMARK 3 S31: 0.2682 S32: 0.0498 S33: 0.2079 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 75 THROUGH 88 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.1756 8.4058 -13.6429 REMARK 3 T TENSOR REMARK 3 T11: 0.0753 T22: 0.0972 REMARK 3 T33: 0.0766 T12: -0.0121 REMARK 3 T13: -0.0064 T23: -0.0053 REMARK 3 L TENSOR REMARK 3 L11: 7.2808 L22: 4.3206 REMARK 3 L33: 2.9219 L12: -3.8365 REMARK 3 L13: -2.5998 L23: 1.3273 REMARK 3 S TENSOR REMARK 3 S11: -0.1071 S12: 0.0085 S13: -0.0443 REMARK 3 S21: -0.1399 S22: 0.1708 S23: 0.0040 REMARK 3 S31: -0.0647 S32: -0.0068 S33: -0.0278 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 89 THROUGH 100 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.6190 15.8711 -25.2435 REMARK 3 T TENSOR REMARK 3 T11: 0.1822 T22: 0.3132 REMARK 3 T33: 0.0838 T12: 0.0614 REMARK 3 T13: -0.0030 T23: 0.0632 REMARK 3 L TENSOR REMARK 3 L11: 7.0307 L22: 5.3016 REMARK 3 L33: 3.5176 L12: -1.6005 REMARK 3 L13: -1.5743 L23: -0.4322 REMARK 3 S TENSOR REMARK 3 S11: -0.3190 S12: 0.2758 S13: -0.1832 REMARK 3 S21: -0.1691 S22: 0.6168 S23: 0.0616 REMARK 3 S31: -0.0323 S32: -1.0334 S33: 0.0015 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 101 THROUGH 117 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.1102 17.3782 -11.3256 REMARK 3 T TENSOR REMARK 3 T11: 0.0841 T22: 0.0765 REMARK 3 T33: 0.1048 T12: -0.0155 REMARK 3 T13: 0.0078 T23: 0.0080 REMARK 3 L TENSOR REMARK 3 L11: 5.6002 L22: 2.4245 REMARK 3 L33: 3.9675 L12: -1.2750 REMARK 3 L13: -0.4477 L23: -0.0177 REMARK 3 S TENSOR REMARK 3 S11: 0.1705 S12: -0.0142 S13: 0.1212 REMARK 3 S21: -0.0247 S22: -0.1689 S23: 0.0023 REMARK 3 S31: -0.2584 S32: -0.0156 S33: 0.0138 REMARK 3 TLS GROUP : 17 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 118 THROUGH 143 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.9522 8.1280 -5.2579 REMARK 3 T TENSOR REMARK 3 T11: 0.0975 T22: 0.1101 REMARK 3 T33: 0.0742 T12: -0.0174 REMARK 3 T13: -0.0089 T23: 0.0351 REMARK 3 L TENSOR REMARK 3 L11: 4.9545 L22: 4.2375 REMARK 3 L33: 2.7637 L12: -1.2550 REMARK 3 L13: -1.2332 L23: 0.5434 REMARK 3 S TENSOR REMARK 3 S11: 0.0546 S12: 0.0624 S13: 0.1468 REMARK 3 S21: 0.0016 S22: -0.0471 S23: -0.2537 REMARK 3 S31: -0.2512 S32: 0.2203 S33: -0.0032 REMARK 3 TLS GROUP : 18 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 144 THROUGH 156 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.6531 2.0835 -3.0818 REMARK 3 T TENSOR REMARK 3 T11: 0.1099 T22: 0.1100 REMARK 3 T33: 0.1003 T12: 0.0106 REMARK 3 T13: 0.0036 T23: 0.0346 REMARK 3 L TENSOR REMARK 3 L11: 6.3030 L22: 6.4023 REMARK 3 L33: 7.2489 L12: -3.6598 REMARK 3 L13: -2.3881 L23: 3.3404 REMARK 3 S TENSOR REMARK 3 S11: -0.1214 S12: 0.2190 S13: -0.5874 REMARK 3 S21: -0.1201 S22: -0.1072 S23: 0.4390 REMARK 3 S31: 0.3753 S32: 0.0479 S33: 0.2260 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 5GHM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1300000790. 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 : 7 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 : 44359 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 47.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: 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 (%): 34.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CITRATE, TRIS, NACL, PH 7, REMARK 280 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 22.89500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.80500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.88900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.80500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.89500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.88900 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: 110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8430 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 22.14 -146.40 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 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 36 O REMARK 620 2 GLU A 56 OE2 72.1 REMARK 620 3 8DG A 201 O1B 109.1 120.3 REMARK 620 4 8DG A 201 O2A 133.1 152.6 67.1 REMARK 620 5 HOH A 310 O 61.2 58.9 70.0 137.0 REMARK 620 6 HOH A 337 O 61.0 70.2 164.2 109.6 111.0 REMARK 620 N 1 2 3 4 5 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 NA A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 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: 5GHI RELATED DB: PDB REMARK 900 RELATED ID: 5GHJ RELATED DB: PDB REMARK 900 RELATED ID: 5GHN RELATED DB: PDB REMARK 900 RELATED ID: 5GHO RELATED DB: PDB REMARK 900 RELATED ID: 5GHP RELATED DB: PDB REMARK 900 RELATED ID: 5GHQ RELATED DB: PDB DBREF 5GHM A 1 156 UNP P36639 8ODP_HUMAN 42 197 DBREF 5GHM B 1 156 UNP P36639 8ODP_HUMAN 42 197 SEQADV 5GHM LYS A 2 UNP P36639 GLY 43 ENGINEERED MUTATION SEQADV 5GHM ASN A 120 UNP P36639 ASP 161 ENGINEERED MUTATION SEQADV 5GHM LYS B 2 UNP P36639 GLY 43 ENGINEERED MUTATION SEQADV 5GHM 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 NA A 202 1 HET 8DG B 201 32 HETNAM 8DG 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE HETNAM NA SODIUM ION FORMUL 3 8DG 2(C10 H16 N5 O14 P3) FORMUL 4 NA NA 1+ FORMUL 6 HOH *382(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 3 TRP A 32 ASN A 33 0 SHEET 2 AA1 3 ARG A 17 LYS A 23 -1 N GLY A 21 O ASN A 33 SHEET 3 AA1 3 MET A 101 GLN A 107 -1 O CYS A 104 N LEU A 20 SHEET 1 AA2 7 TRP A 32 ASN A 33 0 SHEET 2 AA2 7 ARG A 17 LYS A 23 -1 N GLY A 21 O ASN A 33 SHEET 3 AA2 7 SER A 4 LEU A 13 -1 N VAL A 12 O LEU A 19 SHEET 4 AA2 7 LEU A 80 THR A 88 1 O PHE A 86 N LEU A 9 SHEET 5 AA2 7 HIS A 65 PHE A 74 -1 N HIS A 65 O CYS A 87 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 4 TRP B 32 ASN B 33 0 SHEET 2 AA3 4 ARG B 17 LYS B 23 -1 N GLY B 21 O ASN B 33 SHEET 3 AA3 4 SER B 4 LEU B 13 -1 N VAL B 12 O LEU B 19 SHEET 4 AA3 4 MET B 101 GLN B 107 0 SHEET 1 AA4 7 PHE B 35 LYS B 38 0 SHEET 2 AA4 7 SER B 4 LEU B 13 -1 N VAL B 10 O PHE B 35 SHEET 3 AA4 7 ARG B 17 LYS B 23 -1 O LEU B 19 N VAL B 12 SHEET 4 AA4 7 LEU B 80 THR B 88 0 SHEET 5 AA4 7 HIS B 65 PHE B 74 -1 N ILE B 70 O VAL B 83 SHEET 6 AA4 7 PHE B 133 GLN B 140 1 O PHE B 139 N GLU B 73 SHEET 7 AA4 7 THR B 144 GLU B 152 -1 O ASP B 147 N LYS B 138 LINK O GLY A 36 NA NA A 202 1555 1555 2.79 LINK OE2 GLU A 56 NA NA A 202 1555 1555 2.61 LINK O1B 8DG A 201 NA NA A 202 1555 1555 2.52 LINK O2A 8DG A 201 NA NA A 202 1555 1555 2.91 LINK NA NA A 202 O HOH A 310 1555 1555 2.35 LINK NA NA A 202 O HOH A 337 1555 1555 2.38 SITE 1 AC1 13 ASN A 33 GLY A 37 LYS A 38 PHE A 72 SITE 2 AC1 13 MET A 81 TRP A 117 ASP A 119 ASN A 120 SITE 3 AC1 13 PHE A 139 NA A 202 HOH A 310 HOH A 414 SITE 4 AC1 13 LYS B 130 SITE 1 AC2 5 GLY A 36 GLU A 56 8DG A 201 HOH A 310 SITE 2 AC2 5 HOH A 337 SITE 1 AC3 16 PRO A 15 LYS A 130 HOH A 323 TYR B 7 SITE 2 AC3 16 LYS B 23 ASN B 33 LYS B 38 PHE B 72 SITE 3 AC3 16 PHE B 74 MET B 81 TRP B 117 ASP B 119 SITE 4 AC3 16 ASN B 120 PHE B 139 HOH B 302 HOH B 399 CRYST1 45.790 47.778 123.610 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 0.021839 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020930 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008090 0.00000