HEADER HYDROLASE 09-SEP-23 8QHR TITLE CRYSTAL STRUCTURE OF THE HUMAN DNPH1 GLYCOSYL-ENZYME INTERMEDIATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2'-DEOXYNUCLEOSIDE 5'-PHOSPHATE N-HYDROLASE 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: C-MYC-RESPONSIVE PROTEIN RCL; COMPND 5 EC: 3.2.2.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: DNPH1, C6ORF108, RCL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNPH1, N-GLYCOSIDASE, HMDUMP, DRP, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.J.RZECHORZEK,S.C.WEST REVDAT 1 08-NOV-23 8QHR 0 JRNL AUTH N.J.RZECHORZEK,S.KUNZELMANN,A.G.PURKISS,M.SILVA DOS SANTOS, JRNL AUTH 2 J.I.MACRAE,I.A.TAYLOR,K.FUGGER,S.C.WEST JRNL TITL MECHANISM OF SUBSTRATE HYDROLYSIS BY THE HUMAN NUCLEOTIDE JRNL TITL 2 POOL SANITISER DNPH1. JRNL REF NAT COMMUN V. 14 6809 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37884503 JRNL DOI 10.1038/S41467-023-42544-4 REMARK 2 REMARK 2 RESOLUTION. 1.65 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 33391 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1675 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 51.9700 - 3.7800 1.00 2844 144 0.1634 0.1957 REMARK 3 2 3.7800 - 3.0000 1.00 2700 144 0.1418 0.1858 REMARK 3 3 3.0000 - 2.6200 1.00 2655 154 0.1532 0.2044 REMARK 3 4 2.6200 - 2.3800 1.00 2650 149 0.1643 0.1990 REMARK 3 5 2.3800 - 2.2100 1.00 2642 138 0.1672 0.2165 REMARK 3 6 2.2100 - 2.0800 1.00 2608 148 0.1845 0.2165 REMARK 3 7 2.0800 - 1.9700 1.00 2630 139 0.2081 0.2565 REMARK 3 8 1.9700 - 1.8900 0.99 2592 133 0.2354 0.2556 REMARK 3 9 1.8900 - 1.8200 0.99 2614 130 0.2695 0.3033 REMARK 3 10 1.8200 - 1.7500 0.99 2620 133 0.2965 0.2979 REMARK 3 11 1.7500 - 1.7000 0.99 2586 126 0.3161 0.3975 REMARK 3 12 1.7000 - 1.6500 0.98 2575 137 0.3430 0.3366 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) : 0.221 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.329 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.12 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.95 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 : 0.003 2323 REMARK 3 ANGLE : 0.641 3149 REMARK 3 CHIRALITY : 0.042 328 REMARK 3 PLANARITY : 0.010 410 REMARK 3 DIHEDRAL : 6.381 384 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 18 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 49 THROUGH 72 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.4010 -33.0055 -17.8678 REMARK 3 T TENSOR REMARK 3 T11: 0.1862 T22: 0.1521 REMARK 3 T33: 0.1564 T12: -0.0419 REMARK 3 T13: -0.0120 T23: -0.0327 REMARK 3 L TENSOR REMARK 3 L11: 3.9559 L22: 5.6006 REMARK 3 L33: 3.0950 L12: -3.0430 REMARK 3 L13: 2.1306 L23: -2.8385 REMARK 3 S TENSOR REMARK 3 S11: 0.0563 S12: 0.1785 S13: -0.0854 REMARK 3 S21: -0.3944 S22: -0.0163 S23: 0.0712 REMARK 3 S31: 0.3519 S32: 0.0313 S33: -0.0061 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 73 THROUGH 86 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.3100 -25.5883 -14.5876 REMARK 3 T TENSOR REMARK 3 T11: 0.1355 T22: 0.1675 REMARK 3 T33: 0.2157 T12: -0.0185 REMARK 3 T13: 0.0158 T23: -0.0302 REMARK 3 L TENSOR REMARK 3 L11: 1.9466 L22: 3.0507 REMARK 3 L33: 7.7657 L12: -1.8469 REMARK 3 L13: 3.7171 L23: -2.7031 REMARK 3 S TENSOR REMARK 3 S11: -0.2080 S12: -0.1507 S13: -0.0737 REMARK 3 S21: 0.1068 S22: 0.1202 S23: -0.0186 REMARK 3 S31: 0.1200 S32: -0.4160 S33: -0.0156 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 87 THROUGH 110 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.5095 -23.5315 -11.0047 REMARK 3 T TENSOR REMARK 3 T11: 0.1701 T22: 0.1425 REMARK 3 T33: 0.1435 T12: -0.0153 REMARK 3 T13: -0.0020 T23: 0.0065 REMARK 3 L TENSOR REMARK 3 L11: 0.9122 L22: 1.5548 REMARK 3 L33: 0.4157 L12: -0.7771 REMARK 3 L13: 0.1334 L23: -0.0519 REMARK 3 S TENSOR REMARK 3 S11: 0.0574 S12: 0.0877 S13: 0.0600 REMARK 3 S21: 0.0354 S22: -0.0378 S23: 0.0507 REMARK 3 S31: -0.1102 S32: -0.0180 S33: -0.0017 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 111 THROUGH 134 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.8314 -22.7332 -8.7610 REMARK 3 T TENSOR REMARK 3 T11: 0.1401 T22: 0.1461 REMARK 3 T33: 0.0709 T12: 0.0135 REMARK 3 T13: -0.0340 T23: 0.0036 REMARK 3 L TENSOR REMARK 3 L11: 4.6965 L22: 2.8031 REMARK 3 L33: 0.2654 L12: -1.1365 REMARK 3 L13: -1.0942 L23: 0.4300 REMARK 3 S TENSOR REMARK 3 S11: -0.0592 S12: 0.0591 S13: -0.0793 REMARK 3 S21: 0.1927 S22: 0.0224 S23: -0.1122 REMARK 3 S31: 0.0004 S32: -0.0852 S33: 0.0161 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 135 THROUGH 149 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.7264 -28.3925 -5.6097 REMARK 3 T TENSOR REMARK 3 T11: 0.2158 T22: 0.1628 REMARK 3 T33: 0.1398 T12: -0.0019 REMARK 3 T13: -0.0068 T23: 0.0144 REMARK 3 L TENSOR REMARK 3 L11: 1.6387 L22: 3.5399 REMARK 3 L33: 4.7982 L12: -1.4012 REMARK 3 L13: -0.8341 L23: 2.6596 REMARK 3 S TENSOR REMARK 3 S11: -0.1878 S12: -0.1300 S13: -0.0078 REMARK 3 S21: 0.2838 S22: 0.1280 S23: 0.1029 REMARK 3 S31: 0.3874 S32: -0.0803 S33: 0.0688 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 150 THROUGH 159 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.0971 -38.0856 -5.6467 REMARK 3 T TENSOR REMARK 3 T11: 0.2233 T22: 0.1335 REMARK 3 T33: 0.2005 T12: 0.0277 REMARK 3 T13: 0.0006 T23: 0.0546 REMARK 3 L TENSOR REMARK 3 L11: 3.0737 L22: 5.8136 REMARK 3 L33: 5.0996 L12: -0.9401 REMARK 3 L13: -0.8930 L23: 0.5280 REMARK 3 S TENSOR REMARK 3 S11: -0.2609 S12: -0.4210 S13: -0.5567 REMARK 3 S21: 0.6069 S22: -0.0904 S23: -0.1450 REMARK 3 S31: 0.6628 S32: 0.2565 S33: 0.0240 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 18 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.3634 0.1356 -8.3868 REMARK 3 T TENSOR REMARK 3 T11: 0.1499 T22: 0.1934 REMARK 3 T33: 0.1565 T12: -0.0759 REMARK 3 T13: 0.0205 T23: 0.0024 REMARK 3 L TENSOR REMARK 3 L11: 4.7690 L22: 5.1173 REMARK 3 L33: 5.3490 L12: -0.3794 REMARK 3 L13: -0.1655 L23: -0.4954 REMARK 3 S TENSOR REMARK 3 S11: 0.2451 S12: -0.5486 S13: 0.0510 REMARK 3 S21: 0.3446 S22: 0.0951 S23: 0.1362 REMARK 3 S31: -0.4179 S32: 0.0415 S33: -0.2833 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 27 THROUGH 35 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.7639 -9.1964 -18.5750 REMARK 3 T TENSOR REMARK 3 T11: 0.1160 T22: 0.1745 REMARK 3 T33: 0.1707 T12: -0.0168 REMARK 3 T13: 0.0047 T23: 0.0223 REMARK 3 L TENSOR REMARK 3 L11: 2.2741 L22: 4.5878 REMARK 3 L33: 6.1794 L12: -1.3704 REMARK 3 L13: 0.7546 L23: -2.6285 REMARK 3 S TENSOR REMARK 3 S11: -0.0012 S12: -0.1542 S13: 0.1888 REMARK 3 S21: 0.1603 S22: -0.2063 S23: -0.4999 REMARK 3 S31: -0.2221 S32: 0.2089 S33: 0.1184 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 36 THROUGH 48 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.6263 3.3039 -18.9671 REMARK 3 T TENSOR REMARK 3 T11: 0.2101 T22: 0.1338 REMARK 3 T33: 0.1651 T12: -0.0700 REMARK 3 T13: -0.0023 T23: 0.0497 REMARK 3 L TENSOR REMARK 3 L11: 7.2873 L22: 6.2717 REMARK 3 L33: 2.9549 L12: -3.9782 REMARK 3 L13: -1.8440 L23: 1.0662 REMARK 3 S TENSOR REMARK 3 S11: 0.1679 S12: -0.0627 S13: 0.8136 REMARK 3 S21: 0.1121 S22: -0.2346 S23: -0.5784 REMARK 3 S31: -0.5224 S32: 0.1980 S33: -0.0006 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 49 THROUGH 72 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.2881 0.9979 -11.6016 REMARK 3 T TENSOR REMARK 3 T11: 0.1647 T22: 0.1326 REMARK 3 T33: 0.2725 T12: -0.0232 REMARK 3 T13: 0.0262 T23: 0.0504 REMARK 3 L TENSOR REMARK 3 L11: 0.5349 L22: 0.9335 REMARK 3 L33: 3.3155 L12: 0.6314 REMARK 3 L13: 0.5160 L23: -0.1057 REMARK 3 S TENSOR REMARK 3 S11: 0.0602 S12: 0.0741 S13: 0.5217 REMARK 3 S21: -0.0835 S22: -0.2009 S23: -0.8840 REMARK 3 S31: -0.1485 S32: 0.2498 S33: -0.0469 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 73 THROUGH 86 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.3490 -8.1410 -2.0604 REMARK 3 T TENSOR REMARK 3 T11: 0.3193 T22: 0.1704 REMARK 3 T33: 0.1448 T12: -0.0142 REMARK 3 T13: -0.0450 T23: -0.0186 REMARK 3 L TENSOR REMARK 3 L11: 7.0908 L22: 4.7296 REMARK 3 L33: 1.4873 L12: -2.7648 REMARK 3 L13: 2.3292 L23: -2.3300 REMARK 3 S TENSOR REMARK 3 S11: -0.3390 S12: -0.2811 S13: 0.2422 REMARK 3 S21: 0.4370 S22: 0.1962 S23: -0.2502 REMARK 3 S31: -0.2303 S32: 0.0235 S33: 0.1505 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 87 THROUGH 110 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.5589 -10.8525 -12.5685 REMARK 3 T TENSOR REMARK 3 T11: 0.1303 T22: 0.1417 REMARK 3 T33: 0.1220 T12: -0.0085 REMARK 3 T13: -0.0055 T23: 0.0007 REMARK 3 L TENSOR REMARK 3 L11: 0.9265 L22: 1.9268 REMARK 3 L33: 0.9202 L12: -0.6063 REMARK 3 L13: 0.0078 L23: -0.1893 REMARK 3 S TENSOR REMARK 3 S11: -0.0702 S12: -0.0811 S13: 0.0142 REMARK 3 S21: 0.1524 S22: 0.1027 S23: 0.0916 REMARK 3 S31: 0.1561 S32: 0.0205 S33: -0.0076 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 111 THROUGH 128 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.3427 -10.0178 -20.8014 REMARK 3 T TENSOR REMARK 3 T11: 0.1094 T22: 0.1037 REMARK 3 T33: 0.1269 T12: -0.0047 REMARK 3 T13: 0.0001 T23: 0.0142 REMARK 3 L TENSOR REMARK 3 L11: 1.2411 L22: 1.5630 REMARK 3 L33: 5.0616 L12: 0.0961 REMARK 3 L13: -1.0048 L23: -0.1756 REMARK 3 S TENSOR REMARK 3 S11: -0.0079 S12: -0.0448 S13: 0.0252 REMARK 3 S21: -0.0152 S22: 0.1020 S23: 0.1133 REMARK 3 S31: 0.0568 S32: 0.0673 S33: -0.0325 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 129 THROUGH 149 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.9126 -8.9122 -21.5207 REMARK 3 T TENSOR REMARK 3 T11: 0.1306 T22: 0.1412 REMARK 3 T33: 0.1599 T12: -0.0097 REMARK 3 T13: -0.0024 T23: -0.0037 REMARK 3 L TENSOR REMARK 3 L11: 0.5220 L22: 1.6253 REMARK 3 L33: 1.0541 L12: -0.2736 REMARK 3 L13: 0.4747 L23: -0.4334 REMARK 3 S TENSOR REMARK 3 S11: 0.0169 S12: -0.0832 S13: 0.0234 REMARK 3 S21: 0.1173 S22: -0.0370 S23: 0.0638 REMARK 3 S31: 0.0115 S32: -0.0649 S33: 0.0085 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 150 THROUGH 160 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.7527 3.7863 -20.6769 REMARK 3 T TENSOR REMARK 3 T11: 0.1596 T22: 0.1460 REMARK 3 T33: 0.1688 T12: 0.0002 REMARK 3 T13: -0.0020 T23: -0.0038 REMARK 3 L TENSOR REMARK 3 L11: 5.7106 L22: 1.9089 REMARK 3 L33: 8.8948 L12: 0.3174 REMARK 3 L13: 2.3138 L23: -1.4114 REMARK 3 S TENSOR REMARK 3 S11: -0.0449 S12: -0.0763 S13: 0.1940 REMARK 3 S21: -0.1308 S22: 0.1392 S23: 0.2043 REMARK 3 S31: -0.2799 S32: -0.2808 S33: -0.0406 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 19 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.2450 -33.1947 -9.2926 REMARK 3 T TENSOR REMARK 3 T11: 0.2148 T22: 0.1408 REMARK 3 T33: 0.1581 T12: 0.0255 REMARK 3 T13: 0.0128 T23: -0.0168 REMARK 3 L TENSOR REMARK 3 L11: 5.2542 L22: 6.2172 REMARK 3 L33: 3.9731 L12: 2.2129 REMARK 3 L13: -1.2687 L23: -4.9254 REMARK 3 S TENSOR REMARK 3 S11: 0.2495 S12: 0.1670 S13: 0.2131 REMARK 3 S21: 0.2602 S22: 0.0608 S23: 0.7037 REMARK 3 S31: -0.1561 S32: -0.1936 S33: -0.2660 REMARK 3 TLS GROUP : 17 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 27 THROUGH 35 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.6632 -25.2388 -23.3230 REMARK 3 T TENSOR REMARK 3 T11: 0.1706 T22: 0.2208 REMARK 3 T33: 0.1677 T12: 0.0268 REMARK 3 T13: -0.0039 T23: 0.0076 REMARK 3 L TENSOR REMARK 3 L11: 4.2451 L22: 4.6363 REMARK 3 L33: 2.3927 L12: -3.0369 REMARK 3 L13: -0.1126 L23: -0.5459 REMARK 3 S TENSOR REMARK 3 S11: 0.2221 S12: 0.4378 S13: -0.2801 REMARK 3 S21: -0.4640 S22: -0.2411 S23: 0.2103 REMARK 3 S31: 0.2358 S32: 0.0855 S33: 0.0287 REMARK 3 TLS GROUP : 18 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 36 THROUGH 48 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.8446 -37.4667 -16.7637 REMARK 3 T TENSOR REMARK 3 T11: 0.2613 T22: 0.1665 REMARK 3 T33: 0.1805 T12: 0.0369 REMARK 3 T13: 0.0022 T23: -0.0094 REMARK 3 L TENSOR REMARK 3 L11: 1.7991 L22: 4.0461 REMARK 3 L33: 7.8417 L12: 0.9823 REMARK 3 L13: -1.3542 L23: -5.5852 REMARK 3 S TENSOR REMARK 3 S11: -0.0487 S12: 0.1839 S13: -0.1714 REMARK 3 S21: -0.7741 S22: -0.1778 S23: -0.0779 REMARK 3 S31: 0.8939 S32: 0.1837 S33: 0.1541 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 2 REMARK 3 NCS GROUP : ens_1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "B" and resid 41) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "A" and resid 41) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS GROUP : ens_2 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "B" and resid 80) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "A" and resid 80) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8QHR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1292132789. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-APR-22 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 : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8856 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : POINTLESS 1.12.8, AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33501 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 103.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 8.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PROPANE PH 6.5, 16% W/V REMARK 280 PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 23.71000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.97450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.51950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.97450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.71000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.51950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 GLY A 16 REMARK 465 SER A 17 REMARK 465 GLU A 61 REMARK 465 LEU A 62 REMARK 465 GLY A 63 REMARK 465 ALA A 64 REMARK 465 ARG A 65 REMARK 465 GLY A 66 REMARK 465 GLU A 67 REMARK 465 GLU A 68 REMARK 465 ALA A 69 REMARK 465 ALA A 70 REMARK 465 GLY A 71 REMARK 465 ASP A 161 REMARK 465 PRO A 162 REMARK 465 GLY B 16 REMARK 465 SER B 17 REMARK 465 MET B 18 REMARK 465 ALA B 59 REMARK 465 ALA B 60 REMARK 465 GLU B 61 REMARK 465 LEU B 62 REMARK 465 GLY B 63 REMARK 465 ALA B 64 REMARK 465 ARG B 65 REMARK 465 GLY B 66 REMARK 465 GLU B 67 REMARK 465 GLU B 68 REMARK 465 ALA B 160 REMARK 465 ASP B 161 REMARK 465 PRO B 162 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 ILE A 29 -75.16 -125.57 REMARK 500 SER A 128 133.04 -39.35 REMARK 500 SER A 138 -83.94 -132.43 REMARK 500 ILE B 29 -77.79 -125.07 REMARK 500 SER B 128 132.89 -37.19 REMARK 500 SER B 138 -74.57 -136.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 41 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8QHQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN DNPH1 BOUND TO HMDUMP DBREF 8QHR A 19 162 UNP O43598 DNPH1_HUMAN 19 162 DBREF 8QHR B 19 162 UNP O43598 DNPH1_HUMAN 19 162 SEQADV 8QHR GLY A 16 UNP O43598 EXPRESSION TAG SEQADV 8QHR SER A 17 UNP O43598 EXPRESSION TAG SEQADV 8QHR MET A 18 UNP O43598 EXPRESSION TAG SEQADV 8QHR GLN A 55 UNP O43598 GLU 55 ENGINEERED MUTATION SEQADV 8QHR GLY B 16 UNP O43598 EXPRESSION TAG SEQADV 8QHR SER B 17 UNP O43598 EXPRESSION TAG SEQADV 8QHR MET B 18 UNP O43598 EXPRESSION TAG SEQADV 8QHR GLN B 55 UNP O43598 GLU 55 ENGINEERED MUTATION SEQRES 1 A 147 GLY SER MET GLY ARG PRO ALA LEU TYR PHE CYS GLY SER SEQRES 2 A 147 ILE ARG GLY GLY ARG GLU ASP ARG THR LEU TYR GLU ARG SEQRES 3 A 147 ILE VAL SER ARG LEU ARG ARG PHE GLY THR VAL LEU THR SEQRES 4 A 147 GLN HIS VAL ALA ALA ALA GLU LEU GLY ALA ARG GLY GLU SEQRES 5 A 147 GLU ALA ALA GLY GLY ASP ARG LEU ILE HIS GLU GLN ASP SEQRES 6 A 147 LEU GLU TRP LEU GLN GLN ALA ASP VAL VAL VAL ALA GLU SEQRES 7 A 147 VAL THR GLN PRO SER LEU GLY VAL GLY TYR GLU LEU GLY SEQRES 8 A 147 ARG ALA VAL ALA PHE ASN LYS ARG ILE LEU CYS LEU PHE SEQRES 9 A 147 ARG PRO GLN SER GLY ARG VAL LEU SER ALA MET ILE ARG SEQRES 10 A 147 GLY ALA ALA ASP GLY SER ARG PHE GLN VAL TRP ASP TYR SEQRES 11 A 147 GLU GLU GLY GLU VAL GLU ALA LEU LEU ASP ARG TYR PHE SEQRES 12 A 147 GLU ALA ASP PRO SEQRES 1 B 147 GLY SER MET GLY ARG PRO ALA LEU TYR PHE CYS GLY SER SEQRES 2 B 147 ILE ARG GLY GLY ARG GLU ASP ARG THR LEU TYR GLU ARG SEQRES 3 B 147 ILE VAL SER ARG LEU ARG ARG PHE GLY THR VAL LEU THR SEQRES 4 B 147 GLN HIS VAL ALA ALA ALA GLU LEU GLY ALA ARG GLY GLU SEQRES 5 B 147 GLU ALA ALA GLY GLY ASP ARG LEU ILE HIS GLU GLN ASP SEQRES 6 B 147 LEU GLU TRP LEU GLN GLN ALA ASP VAL VAL VAL ALA GLU SEQRES 7 B 147 VAL THR GLN PRO SER LEU GLY VAL GLY TYR GLU LEU GLY SEQRES 8 B 147 ARG ALA VAL ALA PHE ASN LYS ARG ILE LEU CYS LEU PHE SEQRES 9 B 147 ARG PRO GLN SER GLY ARG VAL LEU SER ALA MET ILE ARG SEQRES 10 B 147 GLY ALA ALA ASP GLY SER ARG PHE GLN VAL TRP ASP TYR SEQRES 11 B 147 GLU GLU GLY GLU VAL GLU ALA LEU LEU ASP ARG TYR PHE SEQRES 12 B 147 GLU ALA ASP PRO HET 3DR A 201 40 HET EDO A 202 10 HET EDO A 203 10 HET 3DR B 201 40 HET B3P B 202 45 HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETNAM B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)- HETNAM 2 B3P PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN 3DR ABASIC DIDEOXYRIBOSE HETSYN EDO ETHYLENE GLYCOL FORMUL 3 3DR 2(C5 H11 O6 P) FORMUL 4 EDO 2(C2 H6 O2) FORMUL 7 B3P C11 H26 N2 O6 FORMUL 8 HOH *286(H2 O) HELIX 1 AA1 ASP A 35 ARG A 47 1 13 HELIX 2 AA2 ASP A 73 ALA A 87 1 15 HELIX 3 AA3 SER A 98 PHE A 111 1 14 HELIX 4 AA4 ARG A 120 GLY A 124 5 5 HELIX 5 AA5 SER A 128 GLY A 133 1 6 HELIX 6 AA6 GLU A 149 GLU A 159 1 11 HELIX 7 AA7 ASP B 35 ARG B 47 1 13 HELIX 8 AA8 GLY B 72 ALA B 87 1 16 HELIX 9 AA9 SER B 98 PHE B 111 1 14 HELIX 10 AB1 ARG B 120 GLY B 124 5 5 HELIX 11 AB2 SER B 128 GLY B 133 1 6 HELIX 12 AB3 GLU B 149 GLU B 159 1 11 SHEET 1 AA1 5 THR A 51 THR A 54 0 SHEET 2 AA1 5 ALA A 22 CYS A 26 1 N LEU A 23 O THR A 51 SHEET 3 AA1 5 VAL A 89 GLU A 93 1 O VAL A 91 N TYR A 24 SHEET 4 AA1 5 ARG A 114 PHE A 119 1 O LEU A 116 N VAL A 90 SHEET 5 AA1 5 PHE A 140 ASP A 144 1 O GLN A 141 N CYS A 117 SHEET 1 AA2 5 THR B 51 LEU B 53 0 SHEET 2 AA2 5 ALA B 22 CYS B 26 1 N LEU B 23 O THR B 51 SHEET 3 AA2 5 VAL B 89 GLU B 93 1 O VAL B 91 N TYR B 24 SHEET 4 AA2 5 ARG B 114 PHE B 119 1 O LEU B 116 N VAL B 90 SHEET 5 AA2 5 PHE B 140 ASP B 144 1 O GLN B 141 N CYS B 117 LINK OE2AGLU A 104 C1'A3DR A 201 1555 1555 1.41 LINK OE2BGLU A 104 C1'B3DR A 201 1555 1555 1.41 LINK OE2AGLU B 104 C1'A3DR B 201 1555 1555 1.39 LINK OE2BGLU B 104 C1'B3DR B 201 1555 1555 1.41 CISPEP 1 ARG B 20 PRO B 21 0 1.61 CRYST1 47.420 55.039 103.949 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 0.021088 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018169 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009620 0.00000 MTRIX1 1 -0.172239 -0.016095 -0.984924 1.65049 1 MTRIX2 1 0.026971 -0.999569 0.011618 -34.86325 1 MTRIX3 1 -0.984686 -0.024564 0.172599 1.17389 1 MTRIX1 2 -0.223752 0.021340 -0.974412 4.60396 1 MTRIX2 2 -0.052507 -0.998572 -0.009812 -34.06606 1 MTRIX3 2 -0.973231 0.048969 0.224553 4.15368 1