HEADER HYDROLASE/INHIBITOR 21-AUG-24 9DA6 TITLE CRYSTAL STRUCTURE OF HUMAN DNPH1 BOUND TO INHIBITOR 3A COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5-HYDROXYMETHYL-DUMP N-HYDROLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 2'-DEOXYNUCLEOSIDE 5'-PHOSPHATE N-HYDROLASE 1,C-MYC- COMPND 5 RESPONSIVE PROTEIN RCL; COMPND 6 EC: 3.2.2.-; COMPND 7 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: PRIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-28A(+) KEYWDS INHIBITOR, COMPLEX, HYDROLASE, HYDROLASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.G.WAGNER,V.L.SCHRAMM,S.C.ALMO,A.GHOSH REVDAT 2 26-FEB-25 9DA6 1 JRNL REVDAT 1 05-FEB-25 9DA6 0 JRNL AUTH A.G.WAGNER,T.B.D.LANG,E.T.LEDINGHAM,A.GHOSH,D.BROOKS, JRNL AUTH 2 R.ESKANDARI,K.SUTHAGAR,S.C.ALMO,F.LAMIABLE-OULAIDI, JRNL AUTH 3 P.C.TYLER,V.L.SCHRAMM JRNL TITL TRANSITION STATE ANALOGS OF HUMAN DNPH1 REVEAL TWO JRNL TITL 2 ELECTROPHILE MIGRATION MECHANISMS. JRNL REF J.MED.CHEM. V. 68 3653 2025 JRNL REFN ISSN 0022-2623 JRNL PMID 39818772 JRNL DOI 10.1021/ACS.JMEDCHEM.4C02778 REMARK 2 REMARK 2 RESOLUTION. 1.35 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 56700 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.160 REMARK 3 FREE R VALUE TEST SET COUNT : 2923 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 22.5600 - 3.7100 1.00 2735 131 0.1471 0.1511 REMARK 3 2 3.7100 - 2.9500 1.00 2636 135 0.1517 0.1739 REMARK 3 3 2.9500 - 2.5800 1.00 2581 171 0.1599 0.1650 REMARK 3 4 2.5800 - 2.3400 1.00 2575 133 0.1575 0.2104 REMARK 3 5 2.3400 - 2.1700 1.00 2600 130 0.1459 0.1542 REMARK 3 6 2.1700 - 2.0500 1.00 2546 145 0.1558 0.1681 REMARK 3 7 2.0500 - 1.9400 1.00 2548 133 0.1563 0.1683 REMARK 3 8 1.9400 - 1.8600 1.00 2535 164 0.1653 0.1876 REMARK 3 9 1.8600 - 1.7900 1.00 2543 146 0.1554 0.1665 REMARK 3 10 1.7900 - 1.7300 1.00 2567 131 0.1611 0.1880 REMARK 3 11 1.7300 - 1.6700 1.00 2562 132 0.1599 0.1749 REMARK 3 12 1.6700 - 1.6200 1.00 2575 121 0.1688 0.1876 REMARK 3 13 1.6200 - 1.5800 1.00 2516 140 0.1622 0.1849 REMARK 3 14 1.5800 - 1.5400 1.00 2510 145 0.1682 0.2030 REMARK 3 15 1.5400 - 1.5100 1.00 2567 130 0.1763 0.2373 REMARK 3 16 1.5100 - 1.4800 1.00 2538 162 0.1947 0.2184 REMARK 3 17 1.4800 - 1.4500 1.00 2498 142 0.1995 0.2145 REMARK 3 18 1.4500 - 1.4200 1.00 2559 120 0.2208 0.2327 REMARK 3 19 1.4200 - 1.3900 1.00 2506 139 0.2390 0.2615 REMARK 3 20 1.3900 - 1.3700 1.00 2557 141 0.2407 0.3007 REMARK 3 21 1.3700 - 1.3500 0.99 2523 132 0.2471 0.2548 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.320 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 : 0.008 NULL REMARK 3 ANGLE : 1.169 NULL REMARK 3 CHIRALITY : 0.077 317 REMARK 3 PLANARITY : 0.025 389 REMARK 3 DIHEDRAL : 6.654 316 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 14 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 19 THROUGH 48 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.6442 2.3619 -21.6049 REMARK 3 T TENSOR REMARK 3 T11: 0.0979 T22: 0.1663 REMARK 3 T33: 0.1407 T12: 0.0276 REMARK 3 T13: -0.0114 T23: 0.0228 REMARK 3 L TENSOR REMARK 3 L11: 1.3970 L22: 4.4273 REMARK 3 L33: 2.2232 L12: 0.6384 REMARK 3 L13: -0.5417 L23: -0.7335 REMARK 3 S TENSOR REMARK 3 S11: 0.0168 S12: 0.1854 S13: 0.1246 REMARK 3 S21: -0.1046 S22: 0.0006 S23: -0.0078 REMARK 3 S31: -0.1170 S32: -0.0210 S33: -0.0344 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 49 THROUGH 72 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.6491 1.8147 -26.9982 REMARK 3 T TENSOR REMARK 3 T11: 0.1448 T22: 0.2469 REMARK 3 T33: 0.2513 T12: 0.0464 REMARK 3 T13: -0.0128 T23: 0.0307 REMARK 3 L TENSOR REMARK 3 L11: 3.4044 L22: 2.4373 REMARK 3 L33: 3.3594 L12: 1.0446 REMARK 3 L13: -0.3812 L23: -0.2118 REMARK 3 S TENSOR REMARK 3 S11: 0.1273 S12: -0.0502 S13: 0.3780 REMARK 3 S21: -0.1348 S22: 0.0046 S23: 0.6600 REMARK 3 S31: -0.1835 S32: -0.5507 S33: -0.0617 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 73 THROUGH 85 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.3355 -11.4629 -30.7322 REMARK 3 T TENSOR REMARK 3 T11: 0.2189 T22: 0.2495 REMARK 3 T33: 0.1561 T12: -0.0159 REMARK 3 T13: -0.0087 T23: -0.0174 REMARK 3 L TENSOR REMARK 3 L11: 3.6693 L22: 7.5039 REMARK 3 L33: 3.2951 L12: 5.1344 REMARK 3 L13: 0.4426 L23: -0.3161 REMARK 3 S TENSOR REMARK 3 S11: -0.2977 S12: 0.3421 S13: -0.0174 REMARK 3 S21: -0.4652 S22: 0.1985 S23: 0.1114 REMARK 3 S31: -0.0889 S32: -0.0791 S33: 0.0983 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 86 THROUGH 110 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.6965 -7.5959 -21.5891 REMARK 3 T TENSOR REMARK 3 T11: 0.0820 T22: 0.1644 REMARK 3 T33: 0.1242 T12: 0.0086 REMARK 3 T13: 0.0032 T23: -0.0001 REMARK 3 L TENSOR REMARK 3 L11: 1.5940 L22: 3.9034 REMARK 3 L33: 1.1929 L12: 0.6554 REMARK 3 L13: -0.3448 L23: -0.4342 REMARK 3 S TENSOR REMARK 3 S11: -0.0826 S12: 0.1940 S13: -0.0421 REMARK 3 S21: -0.1740 S22: 0.0700 S23: -0.2159 REMARK 3 S31: 0.1336 S32: 0.0073 S33: 0.0152 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 111 THROUGH 128 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.7322 -3.3878 -14.2569 REMARK 3 T TENSOR REMARK 3 T11: 0.0995 T22: 0.1601 REMARK 3 T33: 0.1707 T12: 0.0061 REMARK 3 T13: -0.0251 T23: -0.0087 REMARK 3 L TENSOR REMARK 3 L11: 0.8141 L22: 3.5597 REMARK 3 L33: 5.5739 L12: 0.0047 REMARK 3 L13: -0.6388 L23: 0.7581 REMARK 3 S TENSOR REMARK 3 S11: -0.0083 S12: 0.0370 S13: 0.0169 REMARK 3 S21: 0.1141 S22: 0.0229 S23: -0.2761 REMARK 3 S31: 0.0109 S32: -0.0230 S33: -0.0177 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 129 THROUGH 146 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.4060 -2.3094 -14.0873 REMARK 3 T TENSOR REMARK 3 T11: 0.1350 T22: 0.1963 REMARK 3 T33: 0.1906 T12: -0.0094 REMARK 3 T13: -0.0310 T23: -0.0170 REMARK 3 L TENSOR REMARK 3 L11: 2.6162 L22: 6.0621 REMARK 3 L33: 1.6552 L12: -0.6025 REMARK 3 L13: 0.5204 L23: -1.6339 REMARK 3 S TENSOR REMARK 3 S11: 0.0431 S12: 0.0782 S13: 0.0466 REMARK 3 S21: 0.0845 S22: -0.0558 S23: -0.7005 REMARK 3 S31: 0.0592 S32: 0.3843 S33: 0.0019 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 147 THROUGH 159 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.3765 9.7594 -18.0008 REMARK 3 T TENSOR REMARK 3 T11: 0.2407 T22: 0.2078 REMARK 3 T33: 0.2225 T12: -0.0282 REMARK 3 T13: -0.0305 T23: -0.0025 REMARK 3 L TENSOR REMARK 3 L11: 8.1900 L22: 8.7401 REMARK 3 L33: 7.8537 L12: -4.2968 REMARK 3 L13: -5.7885 L23: 4.9272 REMARK 3 S TENSOR REMARK 3 S11: 0.0206 S12: -0.3220 S13: 0.3801 REMARK 3 S21: 0.2047 S22: 0.2768 S23: -0.3080 REMARK 3 S31: -0.3958 S32: 0.3841 S33: -0.3310 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 20 THROUGH 48 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.5800 -26.6975 -6.3914 REMARK 3 T TENSOR REMARK 3 T11: 0.3392 T22: 0.1467 REMARK 3 T33: 0.1570 T12: 0.0183 REMARK 3 T13: -0.0067 T23: 0.0140 REMARK 3 L TENSOR REMARK 3 L11: 1.2690 L22: 4.9730 REMARK 3 L33: 1.4251 L12: 0.1095 REMARK 3 L13: -0.4049 L23: -0.4595 REMARK 3 S TENSOR REMARK 3 S11: -0.0971 S12: -0.0338 S13: -0.1769 REMARK 3 S21: 0.1940 S22: 0.0413 S23: -0.1120 REMARK 3 S31: 0.5116 S32: -0.0193 S33: 0.0272 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 49 THROUGH 72 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.3200 -27.1633 -7.6717 REMARK 3 T TENSOR REMARK 3 T11: 0.4050 T22: 0.2680 REMARK 3 T33: 0.3575 T12: 0.1155 REMARK 3 T13: -0.0500 T23: 0.0275 REMARK 3 L TENSOR REMARK 3 L11: 1.7164 L22: 9.1424 REMARK 3 L33: 4.1224 L12: 1.9379 REMARK 3 L13: -0.2367 L23: 1.7354 REMARK 3 S TENSOR REMARK 3 S11: -0.0912 S12: -0.0186 S13: -0.0880 REMARK 3 S21: 0.8181 S22: 0.0903 S23: -1.0221 REMARK 3 S31: 0.5949 S32: 0.4091 S33: 0.0433 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 73 THROUGH 85 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.2685 -18.8787 -12.2477 REMARK 3 T TENSOR REMARK 3 T11: 0.2123 T22: 0.2624 REMARK 3 T33: 0.3619 T12: 0.0618 REMARK 3 T13: -0.0635 T23: 0.0385 REMARK 3 L TENSOR REMARK 3 L11: 4.8854 L22: 6.2382 REMARK 3 L33: 5.0025 L12: 0.5286 REMARK 3 L13: 0.8247 L23: 3.2596 REMARK 3 S TENSOR REMARK 3 S11: 0.0031 S12: 0.0491 S13: -0.2078 REMARK 3 S21: 0.1601 S22: 0.0555 S23: -0.9679 REMARK 3 S31: -0.0682 S32: 0.3263 S33: -0.1022 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 86 THROUGH 110 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.6253 -20.5062 -16.0858 REMARK 3 T TENSOR REMARK 3 T11: 0.1687 T22: 0.1407 REMARK 3 T33: 0.1379 T12: 0.0198 REMARK 3 T13: 0.0011 T23: -0.0049 REMARK 3 L TENSOR REMARK 3 L11: 1.7179 L22: 3.8802 REMARK 3 L33: 2.9132 L12: -0.3541 REMARK 3 L13: -0.4043 L23: 0.4354 REMARK 3 S TENSOR REMARK 3 S11: -0.0640 S12: 0.0463 S13: -0.0519 REMARK 3 S21: 0.0710 S22: 0.0870 S23: -0.2284 REMARK 3 S31: 0.3244 S32: 0.0955 S33: -0.0039 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 111 THROUGH 128 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.1080 -22.3164 -16.4551 REMARK 3 T TENSOR REMARK 3 T11: 0.1851 T22: 0.1326 REMARK 3 T33: 0.0929 T12: -0.0442 REMARK 3 T13: -0.0039 T23: -0.0125 REMARK 3 L TENSOR REMARK 3 L11: 6.5207 L22: 4.7797 REMARK 3 L33: 2.7019 L12: -0.3107 REMARK 3 L13: -0.7151 L23: -0.9226 REMARK 3 S TENSOR REMARK 3 S11: -0.0444 S12: -0.2024 S13: -0.2199 REMARK 3 S21: 0.0593 S22: 0.0324 S23: 0.2824 REMARK 3 S31: 0.3201 S32: -0.0984 S33: 0.0265 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 129 THROUGH 146 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.1152 -24.7091 -21.3829 REMARK 3 T TENSOR REMARK 3 T11: 0.2113 T22: 0.1617 REMARK 3 T33: 0.1542 T12: -0.0267 REMARK 3 T13: 0.0321 T23: -0.0301 REMARK 3 L TENSOR REMARK 3 L11: 2.2009 L22: 4.4717 REMARK 3 L33: 4.5375 L12: 0.5734 REMARK 3 L13: 0.3618 L23: -1.7738 REMARK 3 S TENSOR REMARK 3 S11: -0.0459 S12: 0.1060 S13: -0.2117 REMARK 3 S21: -0.1834 S22: -0.0659 S23: 0.0372 REMARK 3 S31: 0.6086 S32: -0.0343 S33: 0.1231 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 147 THROUGH 159 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.2727 -35.4216 -12.3830 REMARK 3 T TENSOR REMARK 3 T11: 0.5479 T22: 0.1907 REMARK 3 T33: 0.2336 T12: -0.0896 REMARK 3 T13: -0.0439 T23: 0.0355 REMARK 3 L TENSOR REMARK 3 L11: 8.8299 L22: 8.1873 REMARK 3 L33: 7.2262 L12: -3.3832 REMARK 3 L13: -4.6603 L23: 5.0591 REMARK 3 S TENSOR REMARK 3 S11: -0.0211 S12: 0.2506 S13: -0.5283 REMARK 3 S21: -0.1682 S22: 0.1984 S23: 0.2251 REMARK 3 S31: 0.8915 S32: -0.7213 S33: -0.0075 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 9DA6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1000287648. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56772 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 22.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.400 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 9.10 REMARK 200 R MERGE FOR SHELL (I) : 0.75700 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 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% (W/V) PEG 3350, 0.2 M SODIUM REMARK 280 CHLORIDE AND 0.1 M BIS-TRIS, PH 5.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.70350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.70350 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 31.37450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.96250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 31.37450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.96250 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 63.70350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 31.37450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 31.96250 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 63.70350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 31.37450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 31.96250 REMARK 290 SMTRY3 8 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 TOTAL BURIED SURFACE AREA: 2850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL 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 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 HOH A 320 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 423 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 371 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 391 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 SER A 18 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 ALA A 160 REMARK 465 ASP A 161 REMARK 465 PRO A 162 REMARK 465 SER B 18 REMARK 465 MET B 19 REMARK 465 ALA B 58 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 69 REMARK 465 ALA B 70 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 -77.80 -125.25 REMARK 500 SER A 128 132.86 -35.97 REMARK 500 SER A 138 -79.04 -131.55 REMARK 500 ILE B 29 -75.98 -124.42 REMARK 500 SER B 128 130.22 -34.94 REMARK 500 SER B 138 -78.31 -128.29 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 20 0.08 SIDE CHAIN REMARK 500 ARG B 74 0.15 SIDE CHAIN REMARK 500 ARG B 156 0.18 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4P5E RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN DNPH1 (RCL) WITH 6-NAPHTHYL-PURINE- REMARK 900 RIBOSIDE-MONOPHOSPHATE REMARK 900 RELATED ID: 8QHQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN DNPH1 BOUND TO HMDUMP DBREF 9DA6 A 20 162 UNP O43598 DNPH1_HUMAN 20 162 DBREF 9DA6 B 20 162 UNP O43598 DNPH1_HUMAN 20 162 SEQADV 9DA6 SER A 18 UNP O43598 EXPRESSION TAG SEQADV 9DA6 MET A 19 UNP O43598 EXPRESSION TAG SEQADV 9DA6 SER B 18 UNP O43598 EXPRESSION TAG SEQADV 9DA6 MET B 19 UNP O43598 EXPRESSION TAG SEQRES 1 A 145 SER MET ARG PRO ALA LEU TYR PHE CYS GLY SER ILE ARG SEQRES 2 A 145 GLY GLY ARG GLU ASP ARG THR LEU TYR GLU ARG ILE VAL SEQRES 3 A 145 SER ARG LEU ARG ARG PHE GLY THR VAL LEU THR GLU HIS SEQRES 4 A 145 VAL ALA ALA ALA GLU LEU GLY ALA ARG GLY GLU GLU ALA SEQRES 5 A 145 ALA GLY GLY ASP ARG LEU ILE HIS GLU GLN ASP LEU GLU SEQRES 6 A 145 TRP LEU GLN GLN ALA ASP VAL VAL VAL ALA GLU VAL THR SEQRES 7 A 145 GLN PRO SER LEU GLY VAL GLY TYR GLU LEU GLY ARG ALA SEQRES 8 A 145 VAL ALA PHE ASN LYS ARG ILE LEU CYS LEU PHE ARG PRO SEQRES 9 A 145 GLN SER GLY ARG VAL LEU SER ALA MET ILE ARG GLY ALA SEQRES 10 A 145 ALA ASP GLY SER ARG PHE GLN VAL TRP ASP TYR GLU GLU SEQRES 11 A 145 GLY GLU VAL GLU ALA LEU LEU ASP ARG TYR PHE GLU ALA SEQRES 12 A 145 ASP PRO SEQRES 1 B 145 SER MET ARG PRO ALA LEU TYR PHE CYS GLY SER ILE ARG SEQRES 2 B 145 GLY GLY ARG GLU ASP ARG THR LEU TYR GLU ARG ILE VAL SEQRES 3 B 145 SER ARG LEU ARG ARG PHE GLY THR VAL LEU THR GLU HIS SEQRES 4 B 145 VAL ALA ALA ALA GLU LEU GLY ALA ARG GLY GLU GLU ALA SEQRES 5 B 145 ALA GLY GLY ASP ARG LEU ILE HIS GLU GLN ASP LEU GLU SEQRES 6 B 145 TRP LEU GLN GLN ALA ASP VAL VAL VAL ALA GLU VAL THR SEQRES 7 B 145 GLN PRO SER LEU GLY VAL GLY TYR GLU LEU GLY ARG ALA SEQRES 8 B 145 VAL ALA PHE ASN LYS ARG ILE LEU CYS LEU PHE ARG PRO SEQRES 9 B 145 GLN SER GLY ARG VAL LEU SER ALA MET ILE ARG GLY ALA SEQRES 10 B 145 ALA ASP GLY SER ARG PHE GLN VAL TRP ASP TYR GLU GLU SEQRES 11 B 145 GLY GLU VAL GLU ALA LEU LEU ASP ARG TYR PHE GLU ALA SEQRES 12 B 145 ASP PRO HET NR1 A 201 22 HET EDO A 202 10 HET NR1 B 201 22 HETNAM NR1 (3R,4R)-3-HYDROXY-4-[(PHOSPHONOOXY)METHYL]PYRROLIDINIUM HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 NR1 2(C5 H13 N O5 P 1+) FORMUL 4 EDO C2 H6 O2 FORMUL 6 HOH *243(H2 O) HELIX 1 AA1 ASP A 35 ARG A 47 1 13 HELIX 2 AA2 ASP A 73 GLN A 86 1 14 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 146 GLY A 148 5 3 HELIX 7 AA7 GLU A 149 GLU A 159 1 11 HELIX 8 AA8 ASP B 35 ARG B 48 1 14 HELIX 9 AA9 GLY B 72 ALA B 87 1 16 HELIX 10 AB1 SER B 98 PHE B 111 1 14 HELIX 11 AB2 ARG B 120 GLY B 124 5 5 HELIX 12 AB3 SER B 128 GLY B 133 1 6 HELIX 13 AB4 GLU B 146 GLY B 148 5 3 HELIX 14 AB5 GLU B 149 PHE B 158 1 10 SHEET 1 AA1 5 THR A 51 LEU A 53 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 ARG A 114 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 CRYST1 62.749 63.925 127.407 90.00 90.00 90.00 C 2 2 21 16 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 0.015937 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015643 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007849 0.00000