HEADER HYDROLASE 22-MAR-17 5NHY TITLE BAY-707 IN COMPLEX WITH MTH1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 2-HYDROXY-DATP DIPHOSPHATASE,8-OXO-DGTPASE,NUCLEOSIDE COMPND 5 DIPHOSPHATE-LINKED MOIETY X MOTIF 1,NUDIX MOTIF 1; COMPND 6 EC: 3.6.1.55,3.6.1.56; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: FULL LENGTH HUMAN MTH1 ISOFORM P18 CONTAINING COMPND 9 RESIDUALS FROM A THROMBIN-CLEAVAGE SITE IN N-TERMINUS SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 VARIANT: ISOFORM P18; SOURCE 6 GENE: NUDT1, MTH1; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: ROSETTA PHAGE RESISTANT; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET-28A KEYWDS NUDIX, NUCLEOTIDE HYDROLASE, INHIBITOR, ONCOLOGY, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.ELLERMANN,A.EHEIM,A.GIESE,S.BUNSE,K.NOWAK-REPPEL,R.NEUHAUS, AUTHOR 2 J.WEISKE,M.QUANZ,A.GLASAUER,H.MEYER,N.QUEISSER,H.IRLBACHER,B.BADER, AUTHOR 3 F.RAHM,J.VIKLUND,M.ANDERSSON,U.ERICSSON,T.GINMAN,R.FORSBLOM, AUTHOR 4 J.LINDSTROM,C.SILVANDER,L.TRESAUGUES,M.GORJANACZ REVDAT 3 17-JAN-24 5NHY 1 REMARK REVDAT 2 30-AUG-17 5NHY 1 JRNL REVDAT 1 19-JUL-17 5NHY 0 JRNL AUTH M.ELLERMANN,A.EHEIM,F.RAHM,J.VIKLUND,J.GUENTHER,M.ANDERSSON, JRNL AUTH 2 U.ERICSSON,R.FORSBLOM,T.GINMAN,J.LINDSTROM,C.SILVANDER, JRNL AUTH 3 L.TRESAUGUES,A.GIESE,S.BUNSE,R.NEUHAUS,J.WEISKE,M.QUANZ, JRNL AUTH 4 A.GLASAUER,K.NOWAK-REPPEL,B.BADER,H.IRLBACHER,H.MEYER, JRNL AUTH 5 N.QUEISSER,M.BAUSER,A.HAEGEBARTH,M.GORJANACZ JRNL TITL NOVEL CLASS OF POTENT AND CELLULARLY ACTIVE INHIBITORS JRNL TITL 2 DEVALIDATES MTH1 AS BROAD-SPECTRUM CANCER TARGET. JRNL REF ACS CHEM. BIOL. V. 12 1986 2017 JRNL REFN ESSN 1554-8937 JRNL PMID 28679043 JRNL DOI 10.1021/ACSCHEMBIO.7B00370 REMARK 2 REMARK 2 RESOLUTION. 1.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.19 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 33555 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1751 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.72 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2452 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.65 REMARK 3 BIN R VALUE (WORKING SET) : 0.3640 REMARK 3 BIN FREE R VALUE SET COUNT : 112 REMARK 3 BIN FREE R VALUE : 0.3950 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2492 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 95 REMARK 3 SOLVENT ATOMS : 155 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.88 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.15000 REMARK 3 B22 (A**2) : 0.32000 REMARK 3 B33 (A**2) : -0.16000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.135 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.132 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.143 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.498 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2669 ; 0.015 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2423 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3613 ; 1.646 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5625 ; 0.921 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 313 ; 6.503 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 132 ;33.309 ;24.091 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 451 ;14.288 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;10.680 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 376 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2930 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 575 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1231 ; 0.330 ; 0.782 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1230 ; 0.330 ; 0.782 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1536 ; 0.538 ; 1.171 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1537 ; 0.538 ; 1.172 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1438 ; 0.946 ; 1.090 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1438 ; 0.944 ; 1.090 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2073 ; 1.306 ; 1.599 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2879 ; 7.122 ;10.715 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2880 ; 7.121 ;10.740 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 12 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 3 A 24 REMARK 3 ORIGIN FOR THE GROUP (A): -1.5155 14.4271 10.1144 REMARK 3 T TENSOR REMARK 3 T11: 0.0235 T22: 0.0341 REMARK 3 T33: 0.4470 T12: 0.0010 REMARK 3 T13: 0.0227 T23: -0.0081 REMARK 3 L TENSOR REMARK 3 L11: 1.9364 L22: 4.3392 REMARK 3 L33: 1.4086 L12: 0.0004 REMARK 3 L13: 0.4078 L23: 0.5682 REMARK 3 S TENSOR REMARK 3 S11: 0.0605 S12: 0.0247 S13: 0.1002 REMARK 3 S21: 0.0497 S22: 0.0491 S23: 0.1470 REMARK 3 S31: -0.0085 S32: -0.0535 S33: -0.1097 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 25 A 54 REMARK 3 ORIGIN FOR THE GROUP (A): -8.1910 10.6427 12.9195 REMARK 3 T TENSOR REMARK 3 T11: 0.0818 T22: 0.1138 REMARK 3 T33: 0.4434 T12: -0.0245 REMARK 3 T13: 0.0709 T23: 0.0333 REMARK 3 L TENSOR REMARK 3 L11: 7.5693 L22: 6.9443 REMARK 3 L33: 1.8570 L12: 3.3293 REMARK 3 L13: 2.8824 L23: 3.2875 REMARK 3 S TENSOR REMARK 3 S11: 0.1384 S12: -0.4377 S13: -0.0165 REMARK 3 S21: 0.2229 S22: -0.1727 S23: 0.1733 REMARK 3 S31: 0.1139 S32: -0.1956 S33: 0.0343 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 55 A 92 REMARK 3 ORIGIN FOR THE GROUP (A): -2.8917 8.1102 9.3477 REMARK 3 T TENSOR REMARK 3 T11: 0.0435 T22: 0.0239 REMARK 3 T33: 0.4949 T12: -0.0220 REMARK 3 T13: 0.0060 T23: -0.0157 REMARK 3 L TENSOR REMARK 3 L11: 3.8771 L22: 3.5644 REMARK 3 L33: 2.1605 L12: -2.1292 REMARK 3 L13: 0.8850 L23: -1.5184 REMARK 3 S TENSOR REMARK 3 S11: 0.0725 S12: 0.0669 S13: -0.0424 REMARK 3 S21: -0.1614 S22: -0.0910 S23: 0.1471 REMARK 3 S31: 0.0357 S32: -0.0002 S33: 0.0185 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 93 A 100 REMARK 3 ORIGIN FOR THE GROUP (A): -10.0633 23.4675 13.0719 REMARK 3 T TENSOR REMARK 3 T11: 0.2293 T22: 0.2255 REMARK 3 T33: 0.3926 T12: 0.0084 REMARK 3 T13: 0.0359 T23: -0.0320 REMARK 3 L TENSOR REMARK 3 L11: 3.4892 L22: 7.6569 REMARK 3 L33: 29.7929 L12: -0.7255 REMARK 3 L13: 3.5187 L23: -2.0377 REMARK 3 S TENSOR REMARK 3 S11: -0.0081 S12: -0.2101 S13: -0.0702 REMARK 3 S21: -0.2132 S22: 0.0947 S23: 0.5161 REMARK 3 S31: -0.0020 S32: -0.6647 S33: -0.0866 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 101 A 129 REMARK 3 ORIGIN FOR THE GROUP (A): 7.0182 17.6943 11.4534 REMARK 3 T TENSOR REMARK 3 T11: 0.0506 T22: 0.0351 REMARK 3 T33: 0.4668 T12: -0.0186 REMARK 3 T13: 0.0109 T23: 0.0052 REMARK 3 L TENSOR REMARK 3 L11: 2.1733 L22: 4.7962 REMARK 3 L33: 2.0100 L12: -2.1942 REMARK 3 L13: -0.2374 L23: -0.0736 REMARK 3 S TENSOR REMARK 3 S11: -0.0125 S12: 0.0768 S13: 0.2749 REMARK 3 S21: 0.0884 S22: -0.0412 S23: -0.2483 REMARK 3 S31: -0.1304 S32: 0.1401 S33: 0.0537 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 130 A 156 REMARK 3 ORIGIN FOR THE GROUP (A): 9.1590 3.1140 12.0282 REMARK 3 T TENSOR REMARK 3 T11: 0.0099 T22: 0.0070 REMARK 3 T33: 0.4379 T12: 0.0046 REMARK 3 T13: 0.0337 T23: 0.0098 REMARK 3 L TENSOR REMARK 3 L11: 5.3054 L22: 4.0225 REMARK 3 L33: 10.6703 L12: -0.5909 REMARK 3 L13: 2.8108 L23: -1.1834 REMARK 3 S TENSOR REMARK 3 S11: -0.0066 S12: 0.1269 S13: -0.2043 REMARK 3 S21: -0.0765 S22: -0.1033 S23: -0.0492 REMARK 3 S31: 0.0826 S32: 0.0266 S33: 0.1099 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 3 B 31 REMARK 3 ORIGIN FOR THE GROUP (A): 30.8287 -14.8501 9.4718 REMARK 3 T TENSOR REMARK 3 T11: 0.1036 T22: 0.1074 REMARK 3 T33: 1.2703 T12: 0.0073 REMARK 3 T13: -0.1258 T23: -0.1906 REMARK 3 L TENSOR REMARK 3 L11: 14.8574 L22: 4.8183 REMARK 3 L33: 0.5871 L12: 0.5454 REMARK 3 L13: -2.7904 L23: 0.0749 REMARK 3 S TENSOR REMARK 3 S11: 0.0106 S12: 0.2798 S13: -2.7071 REMARK 3 S21: 0.4949 S22: -0.3049 S23: -0.3901 REMARK 3 S31: 0.0387 S32: -0.0091 S33: 0.2943 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 32 B 55 REMARK 3 ORIGIN FOR THE GROUP (A): 38.7177 -9.9066 6.5165 REMARK 3 T TENSOR REMARK 3 T11: 0.3444 T22: 0.2979 REMARK 3 T33: 0.5500 T12: 0.0534 REMARK 3 T13: -0.1695 T23: -0.1003 REMARK 3 L TENSOR REMARK 3 L11: 9.4276 L22: 8.7595 REMARK 3 L33: 0.7004 L12: 2.3695 REMARK 3 L13: -2.4642 L23: 0.0318 REMARK 3 S TENSOR REMARK 3 S11: 0.0343 S12: 0.3114 S13: -1.0330 REMARK 3 S21: -0.0491 S22: -0.2740 S23: -0.1571 REMARK 3 S31: 0.0052 S32: -0.0883 S33: 0.2397 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 56 B 70 REMARK 3 ORIGIN FOR THE GROUP (A): 32.8911 -8.5329 0.6374 REMARK 3 T TENSOR REMARK 3 T11: 0.1872 T22: 0.6280 REMARK 3 T33: 0.6403 T12: -0.0431 REMARK 3 T13: 0.0019 T23: -0.3200 REMARK 3 L TENSOR REMARK 3 L11: 9.7868 L22: 10.0783 REMARK 3 L33: 6.7179 L12: -5.6403 REMARK 3 L13: -7.8604 L23: 3.6534 REMARK 3 S TENSOR REMARK 3 S11: 0.6801 S12: 1.0965 S13: -0.1441 REMARK 3 S21: -0.6722 S22: -0.6006 S23: -0.7424 REMARK 3 S31: -0.5904 S32: -0.5191 S33: -0.0795 REMARK 3 REMARK 3 TLS GROUP : 10 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 71 B 99 REMARK 3 ORIGIN FOR THE GROUP (A): 32.1096 -10.0752 9.7571 REMARK 3 T TENSOR REMARK 3 T11: 0.0265 T22: 0.0667 REMARK 3 T33: 0.9789 T12: -0.0008 REMARK 3 T13: -0.1137 T23: -0.0859 REMARK 3 L TENSOR REMARK 3 L11: 11.1073 L22: 5.6973 REMARK 3 L33: 4.9073 L12: -2.6764 REMARK 3 L13: -5.2889 L23: 2.3912 REMARK 3 S TENSOR REMARK 3 S11: 0.1996 S12: 0.2600 S13: -1.6309 REMARK 3 S21: 0.2171 S22: 0.0124 S23: -0.4141 REMARK 3 S31: -0.0534 S32: 0.0016 S33: -0.2120 REMARK 3 REMARK 3 TLS GROUP : 11 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 100 B 118 REMARK 3 ORIGIN FOR THE GROUP (A): 23.7436 -20.6619 6.8223 REMARK 3 T TENSOR REMARK 3 T11: 0.1336 T22: 0.2824 REMARK 3 T33: 1.7037 T12: -0.1123 REMARK 3 T13: 0.0415 T23: -0.4525 REMARK 3 L TENSOR REMARK 3 L11: 10.8330 L22: 2.8942 REMARK 3 L33: 6.3654 L12: 4.9565 REMARK 3 L13: -0.0284 L23: 1.7855 REMARK 3 S TENSOR REMARK 3 S11: -0.2370 S12: 0.6471 S13: -2.9230 REMARK 3 S21: 0.0685 S22: 0.0288 S23: -1.0474 REMARK 3 S31: 0.4316 S32: -0.3945 S33: 0.2082 REMARK 3 REMARK 3 TLS GROUP : 12 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 119 B 156 REMARK 3 ORIGIN FOR THE GROUP (A): 20.0777 -5.3438 11.8204 REMARK 3 T TENSOR REMARK 3 T11: 0.0472 T22: 0.0417 REMARK 3 T33: 0.5390 T12: 0.0211 REMARK 3 T13: -0.0662 T23: -0.0257 REMARK 3 L TENSOR REMARK 3 L11: 9.9598 L22: 4.2026 REMARK 3 L33: 5.2446 L12: -0.3814 REMARK 3 L13: 0.0614 L23: -2.2435 REMARK 3 S TENSOR REMARK 3 S11: 0.3841 S12: 0.1511 S13: -0.9667 REMARK 3 S21: 0.0498 S22: -0.1843 S23: 0.0020 REMARK 3 S31: 0.1229 S32: -0.0796 S33: -0.1998 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5NHY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1200004161. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.972 REMARK 200 MONOCHROMATOR : SILICON (111) CHANNEL-CUT REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35361 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.720 REMARK 200 RESOLUTION RANGE LOW (A) : 48.190 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 1.29800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 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: 3Q93 REMARK 200 REMARK 200 REMARK: LONG AND LARGE RODS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22.7% PEG4000, 0.24 AMMONIUM SULFATE, REMARK 280 15% GLYCEROL, 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 29.76400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.03750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.35450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.03750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.76400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.35450 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 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 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 GLY A 2 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 GLY B 2 REMARK 465 GLN B 14 REMARK 465 PRO B 15 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 B 308 O HOH B 343 2.02 REMARK 500 O HOH B 301 O HOH B 318 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU B 97 CD GLU B 97 OE1 0.153 REMARK 500 GLU B 97 CD GLU B 97 OE2 0.138 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8XT A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8XT B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 204 DBREF 5NHY A 1 156 UNP P36639 8ODP_HUMAN 1 156 DBREF 5NHY B 1 156 UNP P36639 8ODP_HUMAN 1 156 SEQADV 5NHY GLY A -2 UNP P36639 EXPRESSION TAG SEQADV 5NHY SER A -1 UNP P36639 EXPRESSION TAG SEQADV 5NHY HIS A 0 UNP P36639 EXPRESSION TAG SEQADV 5NHY GLY B -2 UNP P36639 EXPRESSION TAG SEQADV 5NHY SER B -1 UNP P36639 EXPRESSION TAG SEQADV 5NHY HIS B 0 UNP P36639 EXPRESSION TAG SEQRES 1 A 159 GLY SER HIS MET GLY ALA SER ARG LEU TYR THR LEU VAL SEQRES 2 A 159 LEU VAL LEU GLN PRO GLN ARG VAL LEU LEU GLY MET LYS SEQRES 3 A 159 LYS ARG GLY PHE GLY ALA GLY ARG TRP ASN GLY PHE GLY SEQRES 4 A 159 GLY LYS VAL GLN GLU GLY GLU THR ILE GLU ASP GLY ALA SEQRES 5 A 159 ARG ARG GLU LEU GLN GLU GLU SER GLY LEU THR VAL ASP SEQRES 6 A 159 ALA LEU HIS LYS VAL GLY GLN ILE VAL PHE GLU PHE VAL SEQRES 7 A 159 GLY GLU PRO GLU LEU MET ASP VAL HIS VAL PHE CYS THR SEQRES 8 A 159 ASP SER ILE GLN GLY THR PRO VAL GLU SER ASP GLU MET SEQRES 9 A 159 ARG PRO CYS TRP PHE GLN LEU ASP GLN ILE PRO PHE LYS SEQRES 10 A 159 ASP MET TRP PRO ASP ASP SER TYR TRP PHE PRO LEU LEU SEQRES 11 A 159 LEU GLN LYS LYS LYS PHE HIS GLY TYR PHE LYS PHE GLN SEQRES 12 A 159 GLY GLN ASP THR ILE LEU ASP TYR THR LEU ARG GLU VAL SEQRES 13 A 159 ASP THR VAL SEQRES 1 B 159 GLY SER HIS MET GLY ALA SER ARG LEU TYR THR LEU VAL SEQRES 2 B 159 LEU VAL LEU GLN PRO GLN ARG VAL LEU LEU GLY MET LYS SEQRES 3 B 159 LYS ARG GLY PHE GLY ALA GLY ARG TRP ASN GLY PHE GLY SEQRES 4 B 159 GLY LYS VAL GLN GLU GLY GLU THR ILE GLU ASP GLY ALA SEQRES 5 B 159 ARG ARG GLU LEU GLN GLU GLU SER GLY LEU THR VAL ASP SEQRES 6 B 159 ALA LEU HIS LYS VAL GLY GLN ILE VAL PHE GLU PHE VAL SEQRES 7 B 159 GLY GLU PRO GLU LEU MET ASP VAL HIS VAL PHE CYS THR SEQRES 8 B 159 ASP SER ILE GLN GLY THR PRO VAL GLU SER ASP GLU MET SEQRES 9 B 159 ARG PRO CYS TRP PHE GLN LEU ASP GLN ILE PRO PHE LYS SEQRES 10 B 159 ASP MET TRP PRO ASP ASP SER TYR TRP PHE PRO LEU LEU SEQRES 11 B 159 LEU GLN LYS LYS LYS PHE HIS GLY TYR PHE LYS PHE GLN SEQRES 12 B 159 GLY GLN ASP THR ILE LEU ASP TYR THR LEU ARG GLU VAL SEQRES 13 B 159 ASP THR VAL HET 8XT A 201 21 HET SO4 A 202 5 HET SO4 A 203 5 HET SO4 A 204 5 HET SO4 A 205 5 HET SO4 A 206 5 HET SO4 A 207 5 HET GOL A 208 6 HET 8XT B 201 21 HET SO4 B 202 5 HET GOL B 203 6 HET GOL B 204 6 HETNAM 8XT ~{N}-ETHYL-4-[(3~{S})-3-METHYLMORPHOLIN-4-YL]-1~{H}- HETNAM 2 8XT PYRROLO[2,3-B]PYRIDINE-2-CARBOXAMIDE HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 8XT 2(C15 H20 N4 O2) FORMUL 4 SO4 7(O4 S 2-) FORMUL 10 GOL 3(C3 H8 O3) FORMUL 15 HOH *155(H2 O) HELIX 1 AA1 THR A 44 GLY A 58 1 15 HELIX 2 AA2 PRO A 112 MET A 116 5 5 HELIX 3 AA3 TRP A 117 PRO A 118 5 2 HELIX 4 AA4 ASP A 119 GLN A 129 1 11 HELIX 5 AA5 THR B 44 GLY B 58 1 15 HELIX 6 AA6 PRO B 112 MET B 116 5 5 HELIX 7 AA7 TRP B 117 PRO B 118 5 2 HELIX 8 AA8 ASP B 119 GLN B 129 1 11 SHEET 1 AA1 4 TRP A 32 ASN A 33 0 SHEET 2 AA1 4 ARG A 17 LYS A 23 -1 N GLY A 21 O ASN A 33 SHEET 3 AA1 4 SER A 4 GLN A 14 -1 N GLN A 14 O ARG A 17 SHEET 4 AA1 4 MET A 101 GLN A 107 0 SHEET 1 AA212 PHE A 35 LYS A 38 0 SHEET 2 AA212 SER A 4 GLN A 14 -1 N VAL A 10 O PHE A 35 SHEET 3 AA212 ARG A 17 LYS A 23 -1 O ARG A 17 N GLN A 14 SHEET 4 AA212 LEU A 80 THR A 88 0 SHEET 5 AA212 HIS A 65 PHE A 74 -1 N ILE A 70 O VAL A 83 SHEET 6 AA212 LYS A 132 GLN A 140 1 O PHE A 139 N GLU A 73 SHEET 7 AA212 THR A 144 VAL A 153 -1 O LEU A 146 N LYS A 138 SHEET 8 AA212 THR B 144 VAL B 153 1 O GLU B 152 N LEU A 150 SHEET 9 AA212 LYS B 132 GLN B 140 -1 N LYS B 138 O LEU B 146 SHEET 10 AA212 HIS B 65 PHE B 74 1 N GLU B 73 O PHE B 139 SHEET 11 AA212 LEU B 80 THR B 88 -1 O CYS B 87 N HIS B 65 SHEET 12 AA212 SER B 4 VAL B 12 1 N TYR B 7 O HIS B 84 SHEET 1 AA3 2 THR A 60 VAL A 61 0 SHEET 2 AA3 2 ILE A 91 GLN A 92 -1 O GLN A 92 N THR A 60 SHEET 1 AA4 3 TRP B 32 ASN B 33 0 SHEET 2 AA4 3 ARG B 17 LYS B 23 -1 N GLY B 21 O ASN B 33 SHEET 3 AA4 3 MET B 101 GLN B 107 -1 O PHE B 106 N VAL B 18 SITE 1 AC1 10 LEU A 9 ASN A 33 GLY A 34 PHE A 72 SITE 2 AC1 10 MET A 81 MET A 116 TRP A 117 ASP A 119 SITE 3 AC1 10 ASP A 120 TRP A 123 SITE 1 AC2 3 HIS A 65 LYS A 66 HOH A 335 SITE 1 AC3 4 HIS A 134 ARG A 151 HOH A 308 THR B 94 SITE 1 AC4 4 ARG A 17 TRP A 105 SO4 A 207 LYS B 132 SITE 1 AC5 5 ALA A 63 HIS A 65 THR A 88 ASP A 89 SITE 2 AC5 5 SER A 90 SITE 1 AC6 8 LYS A 24 GLU A 97 SER A 98 ASP A 99 SITE 2 AC6 8 TYR B 122 ILE B 145 LEU B 146 TYR B 148 SITE 1 AC7 8 VAL A 75 GLY A 76 PRO A 95 PRO A 103 SITE 2 AC7 8 CYS A 104 TRP A 105 SO4 A 204 HOH A 329 SITE 1 AC8 5 ARG A 151 VAL A 153 ASP A 154 THR A 155 SITE 2 AC8 5 HOH A 334 SITE 1 AC9 10 LEU B 9 ASN B 33 GLY B 34 PHE B 72 SITE 2 AC9 10 MET B 81 MET B 116 TRP B 117 ASP B 119 SITE 3 AC9 10 ASP B 120 PHE B 124 SITE 1 AD1 7 ARG B 151 VAL B 153 ASP B 154 THR B 155 SITE 2 AD1 7 HOH B 305 HOH B 319 HOH B 329 SITE 1 AD2 5 TYR A 148 HIS B 134 ARG B 151 GOL B 204 SITE 2 AD2 5 HOH B 312 SITE 1 AD3 4 GLN B 69 HIS B 134 GLY B 135 GOL B 203 CRYST1 59.528 66.709 82.075 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 0.016799 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014990 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012184 0.00000