HEADER HYDROLASE 24-FEB-21 7NNJ TITLE CRYSTAL STRUCTURE OF NUDT4 (DIPHOSPHOINOSITOL POLYPHOSPHATE TITLE 2 PHOSPHOHYDROLASE 2) IN COMPLEX WITH 4-O-BN-1-PCP-INSP4 (AMR2105) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIPHOSPHOINOSITOL POLYPHOSPHATE PHOSPHOHYDROLASE 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DIPP-2,DIADENOSINE 5',5'''-P1,P6-HEXAPHOSPHATE HYDROLASE 2, COMPND 5 NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 4,NUDIX MOTIF 4; COMPND 6 EC: 3.6.1.52; 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: NUDT4, DIPP2, KIAA0487, HDCMB47P; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NUDIX, HYDROLASE, 1-INSP7 ANALOGUE EXPDTA X-RAY DIFFRACTION AUTHOR Y.DUBIANOK,G.ARRUDA BEZERRA,B.RAUX,L.DIAZ SAEZ,A.M.RILEY, AUTHOR 2 B.V.L.POTTER,K.V.M.HUBER,F.VON DELFT REVDAT 2 31-JAN-24 7NNJ 1 REMARK REVDAT 1 23-MAR-22 7NNJ 0 JRNL AUTH A.M.RILEY,B.RAUX,L.DIAZ SAEZ,Y.DUBIANOK,G.ARRUDA BEZERRA, JRNL AUTH 2 F.VON DELFT,K.V.M.HUBER,B.V.L.POTTER JRNL TITL CRYSTAL STRUCTURE OF NUDT4 (DIPHOSPHOINOSITOL POLYPHOSPHATE JRNL TITL 2 PHOSPHOHYDROLASE 2) IN COMPLEX WITH 4-O-BN-1-PCP-INSP4 JRNL TITL 3 (AMR2105) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 72.6 REMARK 3 NUMBER OF REFLECTIONS : 24359 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1266 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 39.9000 - 3.6498 1.00 3748 235 0.1607 0.1975 REMARK 3 2 3.6498 - 2.8972 1.00 3579 194 0.1863 0.2637 REMARK 3 3 2.8972 - 2.5311 1.00 3526 222 0.2285 0.2451 REMARK 3 4 2.5311 - 2.2997 1.00 3523 199 0.2287 0.3329 REMARK 3 5 2.2997 - 2.1349 0.97 3388 168 0.2370 0.3053 REMARK 3 6 2.1349 - 2.0090 0.77 2718 139 0.2573 0.3261 REMARK 3 7 2.0090 - 1.9084 0.49 1702 72 0.2657 0.3176 REMARK 3 8 1.9084 - 1.8253 0.22 767 32 0.2901 0.2892 REMARK 3 9 1.8253 - 1.7550 0.04 142 5 0.3142 0.3832 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.52 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.38 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 2190 REMARK 3 ANGLE : 1.070 2954 REMARK 3 CHIRALITY : 0.043 315 REMARK 3 PLANARITY : 0.005 372 REMARK 3 DIHEDRAL : 14.794 809 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 17 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 9 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.2190 -17.7180 44.8237 REMARK 3 T TENSOR REMARK 3 T11: 0.3102 T22: 0.1316 REMARK 3 T33: 0.2853 T12: 0.0564 REMARK 3 T13: -0.0614 T23: -0.0102 REMARK 3 L TENSOR REMARK 3 L11: 4.4863 L22: 6.2809 REMARK 3 L33: 6.8357 L12: 5.5763 REMARK 3 L13: 4.1951 L23: 5.4640 REMARK 3 S TENSOR REMARK 3 S11: 0.2959 S12: 0.0260 S13: -0.1195 REMARK 3 S21: 0.3653 S22: -0.1792 S23: -0.0845 REMARK 3 S31: 0.3473 S32: -0.0174 S33: -0.1409 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 27 THROUGH 49 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.9286 -24.6322 34.8249 REMARK 3 T TENSOR REMARK 3 T11: 0.2392 T22: 0.3396 REMARK 3 T33: 0.2712 T12: -0.0253 REMARK 3 T13: -0.1130 T23: 0.0265 REMARK 3 L TENSOR REMARK 3 L11: 9.0551 L22: 7.1213 REMARK 3 L33: 9.2262 L12: -0.9551 REMARK 3 L13: 0.3745 L23: -0.8339 REMARK 3 S TENSOR REMARK 3 S11: 0.2663 S12: 0.0258 S13: -0.2332 REMARK 3 S21: -0.3574 S22: -0.1457 S23: 0.7229 REMARK 3 S31: -0.0639 S32: -1.1930 S33: -0.0083 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 50 THROUGH 79 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.2468 -27.1033 46.2551 REMARK 3 T TENSOR REMARK 3 T11: 0.2515 T22: 0.1170 REMARK 3 T33: 0.2135 T12: -0.0059 REMARK 3 T13: -0.0652 T23: 0.0031 REMARK 3 L TENSOR REMARK 3 L11: 4.5310 L22: 3.7393 REMARK 3 L33: 5.4797 L12: 0.0196 REMARK 3 L13: -0.0584 L23: -1.7114 REMARK 3 S TENSOR REMARK 3 S11: 0.1776 S12: -0.2484 S13: -0.1424 REMARK 3 S21: 0.2877 S22: -0.0245 S23: -0.1425 REMARK 3 S31: 0.0065 S32: -0.2446 S33: -0.1853 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 80 THROUGH 90 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.2435 -14.5188 37.8487 REMARK 3 T TENSOR REMARK 3 T11: 0.4772 T22: 0.1902 REMARK 3 T33: 0.2896 T12: -0.0334 REMARK 3 T13: -0.0092 T23: 0.0519 REMARK 3 L TENSOR REMARK 3 L11: 6.0081 L22: 10.1107 REMARK 3 L33: 8.7929 L12: -2.1573 REMARK 3 L13: 1.6458 L23: 5.4206 REMARK 3 S TENSOR REMARK 3 S11: -0.4575 S12: 0.1713 S13: 0.6265 REMARK 3 S21: -0.4827 S22: 0.2753 S23: 0.4821 REMARK 3 S31: -1.5960 S32: 0.2580 S33: 0.3417 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 91 THROUGH 115 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.8364 -27.7648 40.9362 REMARK 3 T TENSOR REMARK 3 T11: 0.3466 T22: 0.2371 REMARK 3 T33: 0.3543 T12: -0.0272 REMARK 3 T13: -0.0367 T23: 0.0067 REMARK 3 L TENSOR REMARK 3 L11: 3.4577 L22: 4.8386 REMARK 3 L33: 5.0483 L12: 1.6940 REMARK 3 L13: 1.3089 L23: -0.8277 REMARK 3 S TENSOR REMARK 3 S11: 0.4629 S12: -0.1880 S13: -0.0365 REMARK 3 S21: 0.4440 S22: -0.1181 S23: 0.7564 REMARK 3 S31: 0.4944 S32: -0.6752 S33: -0.3359 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 116 THROUGH 132 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.4998 -22.2693 29.2175 REMARK 3 T TENSOR REMARK 3 T11: 0.3086 T22: 0.3784 REMARK 3 T33: 0.3664 T12: 0.0481 REMARK 3 T13: -0.1123 T23: 0.0533 REMARK 3 L TENSOR REMARK 3 L11: 5.5296 L22: 7.3074 REMARK 3 L33: 8.7412 L12: -0.0532 REMARK 3 L13: 1.2971 L23: 1.3938 REMARK 3 S TENSOR REMARK 3 S11: 0.0673 S12: 0.1287 S13: 0.2098 REMARK 3 S21: -0.6108 S22: -0.0128 S23: 0.7956 REMARK 3 S31: -0.4126 S32: -1.0228 S33: -0.0261 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 133 THROUGH 146 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.7771 -19.3119 29.5021 REMARK 3 T TENSOR REMARK 3 T11: 0.3672 T22: 0.2742 REMARK 3 T33: 0.2096 T12: 0.0094 REMARK 3 T13: -0.0728 T23: 0.0552 REMARK 3 L TENSOR REMARK 3 L11: 8.3966 L22: 6.9475 REMARK 3 L33: 7.2654 L12: -3.1170 REMARK 3 L13: -2.4065 L23: 2.8002 REMARK 3 S TENSOR REMARK 3 S11: 0.1313 S12: 0.6538 S13: 0.0723 REMARK 3 S21: -0.4963 S22: -0.0180 S23: 0.1323 REMARK 3 S31: -0.6814 S32: 0.1944 S33: -0.1418 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 8 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.7966 -8.7175 3.7030 REMARK 3 T TENSOR REMARK 3 T11: 0.2366 T22: 0.6508 REMARK 3 T33: 0.3381 T12: 0.0284 REMARK 3 T13: -0.0232 T23: 0.0585 REMARK 3 L TENSOR REMARK 3 L11: 3.9864 L22: 1.0108 REMARK 3 L33: 4.4067 L12: 0.0729 REMARK 3 L13: -4.6748 L23: -0.3713 REMARK 3 S TENSOR REMARK 3 S11: -0.1149 S12: 0.2363 S13: -0.2001 REMARK 3 S21: 0.0578 S22: 0.0868 S23: -0.0863 REMARK 3 S31: -0.1538 S32: -0.2032 S33: 0.0848 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 27 THROUGH 32 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.9848 -5.5217 23.3040 REMARK 3 T TENSOR REMARK 3 T11: 0.6469 T22: 0.8586 REMARK 3 T33: 0.5947 T12: 0.3692 REMARK 3 T13: 0.2495 T23: 0.0519 REMARK 3 L TENSOR REMARK 3 L11: 8.6916 L22: 9.1804 REMARK 3 L33: 2.0529 L12: 0.2509 REMARK 3 L13: 5.0910 L23: -8.2046 REMARK 3 S TENSOR REMARK 3 S11: -0.3073 S12: -0.0892 S13: 0.5724 REMARK 3 S21: 0.1934 S22: -0.3246 S23: 0.7890 REMARK 3 S31: 0.1116 S32: -0.6159 S33: 0.4057 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 33 THROUGH 49 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.5685 -16.8751 20.5787 REMARK 3 T TENSOR REMARK 3 T11: 0.4105 T22: 0.6104 REMARK 3 T33: 0.4303 T12: 0.1081 REMARK 3 T13: -0.0519 T23: 0.0073 REMARK 3 L TENSOR REMARK 3 L11: 2.9392 L22: 3.6596 REMARK 3 L33: 5.2279 L12: -1.5816 REMARK 3 L13: 3.6144 L23: -1.8197 REMARK 3 S TENSOR REMARK 3 S11: 0.2388 S12: 0.1573 S13: -0.4270 REMARK 3 S21: 0.1324 S22: 0.1705 S23: -0.5357 REMARK 3 S31: 0.2771 S32: 0.4295 S33: -0.3992 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 50 THROUGH 58 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.6100 -12.2929 -0.1824 REMARK 3 T TENSOR REMARK 3 T11: 0.0887 T22: 0.9197 REMARK 3 T33: 0.3300 T12: 0.0751 REMARK 3 T13: 0.0384 T23: 0.1590 REMARK 3 L TENSOR REMARK 3 L11: 4.5901 L22: 5.1959 REMARK 3 L33: 7.6975 L12: 0.4829 REMARK 3 L13: 1.7128 L23: 3.7831 REMARK 3 S TENSOR REMARK 3 S11: -1.4225 S12: -0.0761 S13: -0.6844 REMARK 3 S21: -1.1810 S22: 1.2755 S23: -0.2445 REMARK 3 S31: 0.1137 S32: 0.1632 S33: 0.0251 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 59 THROUGH 79 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.6197 -13.7208 9.5367 REMARK 3 T TENSOR REMARK 3 T11: 0.2253 T22: 0.5396 REMARK 3 T33: 0.3930 T12: 0.0732 REMARK 3 T13: 0.0083 T23: 0.0989 REMARK 3 L TENSOR REMARK 3 L11: 0.6550 L22: 3.2572 REMARK 3 L33: 3.4579 L12: 1.7991 REMARK 3 L13: -0.3973 L23: -0.5607 REMARK 3 S TENSOR REMARK 3 S11: -0.2086 S12: -0.0012 S13: -0.1231 REMARK 3 S21: 0.0728 S22: 0.3886 S23: 0.1165 REMARK 3 S31: 0.1258 S32: -0.2757 S33: -0.1837 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 80 THROUGH 90 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.4514 -2.8680 9.3258 REMARK 3 T TENSOR REMARK 3 T11: 0.2416 T22: 0.6885 REMARK 3 T33: 0.3861 T12: -0.0208 REMARK 3 T13: -0.0817 T23: -0.0709 REMARK 3 L TENSOR REMARK 3 L11: 0.7395 L22: 6.6215 REMARK 3 L33: 4.1825 L12: -0.7416 REMARK 3 L13: 1.5470 L23: -2.5852 REMARK 3 S TENSOR REMARK 3 S11: -0.9978 S12: -1.0928 S13: 0.6850 REMARK 3 S21: -0.5028 S22: 1.5828 S23: -1.3311 REMARK 3 S31: -1.7297 S32: 1.9874 S33: 0.0298 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 91 THROUGH 103 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.3165 -8.7604 11.3679 REMARK 3 T TENSOR REMARK 3 T11: 0.2627 T22: 0.6851 REMARK 3 T33: 0.2968 T12: 0.1269 REMARK 3 T13: -0.0571 T23: 0.0871 REMARK 3 L TENSOR REMARK 3 L11: 0.3720 L22: 5.1892 REMARK 3 L33: 4.5929 L12: -0.0972 REMARK 3 L13: -1.5183 L23: -2.2162 REMARK 3 S TENSOR REMARK 3 S11: -0.0057 S12: 0.8220 S13: 0.0918 REMARK 3 S21: 0.2600 S22: 0.4861 S23: 0.3789 REMARK 3 S31: -0.1708 S32: -0.2349 S33: -0.4213 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 104 THROUGH 116 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.7167 -25.0040 16.4163 REMARK 3 T TENSOR REMARK 3 T11: 0.4227 T22: 0.7088 REMARK 3 T33: 0.8201 T12: 0.0271 REMARK 3 T13: 0.0059 T23: -0.0840 REMARK 3 L TENSOR REMARK 3 L11: 3.0256 L22: 0.2041 REMARK 3 L33: 0.6162 L12: -0.8655 REMARK 3 L13: 1.2314 L23: -0.4386 REMARK 3 S TENSOR REMARK 3 S11: 0.7165 S12: 1.4881 S13: -1.5769 REMARK 3 S21: -0.5568 S22: 0.0020 S23: -0.1990 REMARK 3 S31: 0.4228 S32: 0.6061 S33: -0.6799 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 117 THROUGH 129 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.8029 -10.5656 26.1234 REMARK 3 T TENSOR REMARK 3 T11: 0.5581 T22: 0.5922 REMARK 3 T33: 0.3100 T12: 0.1525 REMARK 3 T13: 0.0176 T23: 0.1184 REMARK 3 L TENSOR REMARK 3 L11: 8.2856 L22: 8.1509 REMARK 3 L33: 3.7643 L12: 5.0046 REMARK 3 L13: 1.3488 L23: 1.4535 REMARK 3 S TENSOR REMARK 3 S11: 0.0937 S12: -0.8085 S13: -0.1808 REMARK 3 S21: 1.2382 S22: -0.1231 S23: 0.1793 REMARK 3 S31: -0.2802 S32: -0.1251 S33: -0.0326 REMARK 3 TLS GROUP : 17 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 130 THROUGH 145 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.7988 -3.8354 19.9684 REMARK 3 T TENSOR REMARK 3 T11: 0.3944 T22: 0.4482 REMARK 3 T33: 0.4785 T12: 0.0355 REMARK 3 T13: -0.0947 T23: 0.0479 REMARK 3 L TENSOR REMARK 3 L11: 3.1650 L22: 2.7988 REMARK 3 L33: 4.3469 L12: -5.9484 REMARK 3 L13: -0.0900 L23: -1.3658 REMARK 3 S TENSOR REMARK 3 S11: -0.1358 S12: -0.4955 S13: 0.4451 REMARK 3 S21: 0.7474 S22: 0.1395 S23: -0.7596 REMARK 3 S31: -0.2680 S32: 0.2215 S33: -0.0575 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 7NNJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1292114127. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AIMLESS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24365 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.755 REMARK 200 RESOLUTION RANGE LOW (A) : 98.844 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 200 DATA REDUNDANCY : 25.30 REMARK 200 R MERGE (I) : 0.10300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 56.1 REMARK 200 DATA REDUNDANCY IN SHELL : 25.10 REMARK 200 R MERGE FOR SHELL (I) : 2.70000 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 2.5.6 REMARK 200 STARTING MODEL: 5TLU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.75 M SODIUM FORMATE, PH 7.5, VAPOR REMARK 280 DIFFUSION, SITTING 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 20.09050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 98.84400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.38600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 98.84400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.09050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.38600 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 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 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 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 7 REMARK 465 MET A 8 REMARK 465 GLU A 108 REMARK 465 ASP A 109 REMARK 465 SER A 110 REMARK 465 VAL A 111 REMARK 465 ASN A 112 REMARK 465 ILE A 113 REMARK 465 GLY A 114 REMARK 465 SER B 7 REMARK 465 GLU B 108 REMARK 465 ASP B 109 REMARK 465 SER B 110 REMARK 465 VAL B 111 REMARK 465 ASN B 112 REMARK 465 GLY B 146 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 29 CG CD OE1 OE2 REMARK 470 SER A 40 OG REMARK 470 ARG A 41 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 44 CG OD1 OD2 REMARK 470 LYS A 74 CG CD CE NZ REMARK 470 LYS A 76 CG CD CE NZ REMARK 470 ASP A 88 CG OD1 OD2 REMARK 470 GLU A 102 CG CD OE1 OE2 REMARK 470 LEU A 104 CG CD1 CD2 REMARK 470 ASP A 106 CG OD1 OD2 REMARK 470 ARG A 115 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 116 CG CD CE NZ REMARK 470 LYS A 121 CG CD CE NZ REMARK 470 GLU B 29 CG CD OE1 OE2 REMARK 470 LYS B 74 CG CD CE NZ REMARK 470 LYS B 76 CG CD CE NZ REMARK 470 GLN B 87 CG CD OE1 NE2 REMARK 470 ASP B 88 CG OD1 OD2 REMARK 470 GLU B 105 CG CD OE1 OE2 REMARK 470 LYS B 116 CG CD CE NZ REMARK 470 LYS B 127 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 313 O HOH A 324 2.10 REMARK 500 O HOH B 302 O HOH B 309 2.18 REMARK 500 O HOH B 336 O HOH B 344 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG B 89 NE - CZ - NH2 ANGL. DEV. = 4.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS A 133 79.54 -161.03 REMARK 500 GLU B 56 -6.16 69.12 REMARK 500 LYS B 144 23.87 -77.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5TLU RELATED DB: PDB REMARK 900 PROTEIN STRUCTURE DBREF 7NNJ A 9 146 UNP Q9NZJ9 NUDT4_HUMAN 9 146 DBREF 7NNJ B 9 146 UNP Q9NZJ9 NUDT4_HUMAN 9 146 SEQADV 7NNJ SER A 7 UNP Q9NZJ9 EXPRESSION TAG SEQADV 7NNJ MET A 8 UNP Q9NZJ9 EXPRESSION TAG SEQADV 7NNJ SER B 7 UNP Q9NZJ9 EXPRESSION TAG SEQADV 7NNJ MET B 8 UNP Q9NZJ9 EXPRESSION TAG SEQRES 1 A 140 SER MET THR ARG THR TYR ASP ARG GLU GLY PHE LYS LYS SEQRES 2 A 140 ARG ALA ALA CYS LEU CYS PHE ARG SER GLU GLN GLU ASP SEQRES 3 A 140 GLU VAL LEU LEU VAL SER SER SER ARG TYR PRO ASP GLN SEQRES 4 A 140 TRP ILE VAL PRO GLY GLY GLY MET GLU PRO GLU GLU GLU SEQRES 5 A 140 PRO GLY GLY ALA ALA VAL ARG GLU VAL TYR GLU GLU ALA SEQRES 6 A 140 GLY VAL LYS GLY LYS LEU GLY ARG LEU LEU GLY ILE PHE SEQRES 7 A 140 GLU ASN GLN ASP ARG LYS HIS ARG THR TYR VAL TYR VAL SEQRES 8 A 140 LEU THR VAL THR GLU ILE LEU GLU ASP TRP GLU ASP SER SEQRES 9 A 140 VAL ASN ILE GLY ARG LYS ARG GLU TRP PHE LYS VAL GLU SEQRES 10 A 140 ASP ALA ILE LYS VAL LEU GLN CYS HIS LYS PRO VAL HIS SEQRES 11 A 140 ALA GLU TYR LEU GLU LYS LEU LYS LEU GLY SEQRES 1 B 140 SER MET THR ARG THR TYR ASP ARG GLU GLY PHE LYS LYS SEQRES 2 B 140 ARG ALA ALA CYS LEU CYS PHE ARG SER GLU GLN GLU ASP SEQRES 3 B 140 GLU VAL LEU LEU VAL SER SER SER ARG TYR PRO ASP GLN SEQRES 4 B 140 TRP ILE VAL PRO GLY GLY GLY MET GLU PRO GLU GLU GLU SEQRES 5 B 140 PRO GLY GLY ALA ALA VAL ARG GLU VAL TYR GLU GLU ALA SEQRES 6 B 140 GLY VAL LYS GLY LYS LEU GLY ARG LEU LEU GLY ILE PHE SEQRES 7 B 140 GLU ASN GLN ASP ARG LYS HIS ARG THR TYR VAL TYR VAL SEQRES 8 B 140 LEU THR VAL THR GLU ILE LEU GLU ASP TRP GLU ASP SER SEQRES 9 B 140 VAL ASN ILE GLY ARG LYS ARG GLU TRP PHE LYS VAL GLU SEQRES 10 B 140 ASP ALA ILE LYS VAL LEU GLN CYS HIS LYS PRO VAL HIS SEQRES 11 B 140 ALA GLU TYR LEU GLU LYS LEU LYS LEU GLY HET EDO A 201 4 HET EDO A 202 4 HET FMT A 203 3 HET FMT A 204 3 HET FMT A 205 3 HET EDO B 201 4 HET FMT B 202 3 HET FMT B 203 3 HET UJN B 204 43 HETNAM EDO 1,2-ETHANEDIOL HETNAM FMT FORMIC ACID HETNAM UJN [OXIDANYL-[(2S,3R,5S,6S)-4-PHENYLMETHOXY-2,3,5,6- HETNAM 2 UJN TETRAPHOSPHONOOXY-CYCLOHEXYL]OXY- HETNAM 3 UJN PHOSPHORYL]METHYLPHOSPHONIC ACID HETSYN EDO ETHYLENE GLYCOL HETSYN UJN [OXIDANYL-[(2~{S},3~{R},5~{S},6~{S})-4-PHENYLMETHOXY-2, HETSYN 2 UJN 3,5,6-TETRAPHOSPHONOOXY-CYCLOHEXYL]OXY- HETSYN 3 UJN PHOSPHORYL]METHYLPHOSPHONIC ACID FORMUL 3 EDO 3(C2 H6 O2) FORMUL 5 FMT 5(C H2 O2) FORMUL 11 UJN C14 H26 O23 P6 FORMUL 12 HOH *105(H2 O) HELIX 1 AA1 GLU A 58 GLY A 72 1 15 HELIX 2 AA2 VAL A 122 LYS A 133 1 12 HELIX 3 AA3 LYS A 133 GLY A 146 1 14 HELIX 4 AA4 GLU B 58 GLY B 72 1 15 HELIX 5 AA5 VAL B 122 GLN B 130 1 9 HELIX 6 AA6 LYS B 133 LYS B 144 1 12 SHEET 1 AA1 4 GLY A 50 GLY A 52 0 SHEET 2 AA1 4 LYS A 18 PHE A 26 -1 N ALA A 21 O GLY A 51 SHEET 3 AA1 4 HIS A 91 ILE A 103 1 O LEU A 98 N PHE A 26 SHEET 4 AA1 4 VAL A 73 ASN A 86 -1 N GLY A 78 O VAL A 97 SHEET 1 AA2 2 GLU A 33 SER A 38 0 SHEET 2 AA2 2 LYS A 116 LYS A 121 -1 O PHE A 120 N VAL A 34 SHEET 1 AA3 5 TRP B 46 ILE B 47 0 SHEET 2 AA3 5 GLU B 33 SER B 38 -1 N VAL B 37 O ILE B 47 SHEET 3 AA3 5 LYS B 18 PHE B 26 -1 N CYS B 25 O LEU B 35 SHEET 4 AA3 5 HIS B 91 ILE B 103 1 O TYR B 96 N LEU B 24 SHEET 5 AA3 5 VAL B 73 ASN B 86 -1 N GLY B 78 O VAL B 97 SHEET 1 AA4 4 GLY B 50 GLY B 52 0 SHEET 2 AA4 4 LYS B 18 PHE B 26 -1 N ALA B 21 O GLY B 51 SHEET 3 AA4 4 GLU B 33 SER B 38 -1 O LEU B 35 N CYS B 25 SHEET 4 AA4 4 ARG B 117 LYS B 121 -1 O PHE B 120 N VAL B 34 SSBOND 1 CYS A 131 CYS B 131 1555 1455 2.01 CRYST1 40.181 40.772 197.688 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 0.024887 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024527 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005058 0.00000