HEADER HYDROLASE/HYDROLASE INHIBITOR 26-APR-11 3ROP TITLE CRYSTAL STRUCTURE OF HUMAN CD38 IN COMPLEX WITH COMPOUND CZ-50B COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADP-RIBOSYL CYCLASE 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: ECTODOMAIN (UNP RESIDUES 45-296); COMPND 5 SYNONYM: CYCLIC ADP-RIBOSE HYDROLASE 1, CADPR HYDROLASE 1, T10; COMPND 6 EC: 3.2.2.5; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CD38; SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: X33; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPICZALPHA KEYWDS CD38, ADP-RIBOSYL CYCLASE, CYCLIC ADP-RIBOSE, X-CRYSTALLOGRAPHY, KEYWDS 2 CALCIUM SIGNALING, INHIBITORY COMPOUND, COVALENT INTERMEDIATE, CZ- KEYWDS 3 50B, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.ZHANG,H.C.LEE,Q.HAO REVDAT 4 01-NOV-23 3ROP 1 HETSYN REVDAT 3 29-JUL-20 3ROP 1 REMARK SEQADV LINK SITE REVDAT 2 03-JUL-13 3ROP 1 JRNL HETNAM FORMUL HETATM REVDAT 2 2 1 HETSYN REVDAT 1 28-DEC-11 3ROP 0 JRNL AUTH A.K.KWONG,Z.CHEN,H.ZHANG,F.P.LEUNG,C.M.LAM,K.Y.TING,L.ZHANG, JRNL AUTH 2 Q.HAO,L.H.ZHANG,H.C.LEE JRNL TITL CATALYSIS-BASED INHIBITORS OF THE CALCIUM SIGNALING FUNCTION JRNL TITL 2 OF CD38. JRNL REF BIOCHEMISTRY V. 51 555 2012 JRNL REFN ISSN 0006-2960 JRNL PMID 22142305 JRNL DOI 10.1021/BI201509F REMARK 2 REMARK 2 RESOLUTION. 1.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 35482 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1891 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) : 1.94 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.99 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2358 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.76 REMARK 3 BIN R VALUE (WORKING SET) : 0.2110 REMARK 3 BIN FREE R VALUE SET COUNT : 111 REMARK 3 BIN FREE R VALUE : 0.2540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4086 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 266 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.72000 REMARK 3 B22 (A**2) : 2.38000 REMARK 3 B33 (A**2) : -0.40000 REMARK 3 B12 (A**2) : 0.07000 REMARK 3 B13 (A**2) : 0.51000 REMARK 3 B23 (A**2) : 0.33000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.171 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.146 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.102 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.537 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4245 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2924 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5756 ; 1.198 ; 1.945 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7102 ; 0.827 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 502 ; 5.530 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 206 ;34.264 ;24.175 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 736 ;13.398 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;19.672 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 616 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4652 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 874 ; 0.001 ; 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): 2520 ; 0.538 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1002 ; 0.136 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4108 ; 1.084 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1725 ; 1.815 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1648 ; 2.912 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 45 A 55 REMARK 3 ORIGIN FOR THE GROUP (A): 11.0650 -9.4920 60.3080 REMARK 3 T TENSOR REMARK 3 T11: 0.4741 T22: 0.7020 REMARK 3 T33: 0.9122 T12: 0.2811 REMARK 3 T13: -0.1995 T23: 0.2551 REMARK 3 L TENSOR REMARK 3 L11: 55.5756 L22: 45.5565 REMARK 3 L33: 84.2069 L12: -50.3099 REMARK 3 L13: 68.4052 L23: -61.9288 REMARK 3 S TENSOR REMARK 3 S11: 1.1487 S12: 0.7391 S13: -0.2822 REMARK 3 S21: -1.0707 S22: -0.7714 S23: 0.1474 REMARK 3 S31: 1.5203 S32: 0.9941 S33: -0.3774 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 56 A 79 REMARK 3 ORIGIN FOR THE GROUP (A): -16.6970 -9.1160 50.8120 REMARK 3 T TENSOR REMARK 3 T11: 0.1743 T22: 0.1316 REMARK 3 T33: 0.4619 T12: -0.0228 REMARK 3 T13: -0.0404 T23: -0.0158 REMARK 3 L TENSOR REMARK 3 L11: 17.2127 L22: 6.9613 REMARK 3 L33: 4.2901 L12: -2.1235 REMARK 3 L13: 4.7999 L23: -1.9687 REMARK 3 S TENSOR REMARK 3 S11: 0.6293 S12: -0.1683 S13: -1.5523 REMARK 3 S21: -0.1594 S22: 0.0061 S23: 0.6634 REMARK 3 S31: 0.4801 S32: -0.5322 S33: -0.6354 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 80 A 124 REMARK 3 ORIGIN FOR THE GROUP (A): -7.6570 -3.1080 43.3780 REMARK 3 T TENSOR REMARK 3 T11: 0.1753 T22: 0.2867 REMARK 3 T33: 0.3419 T12: 0.0712 REMARK 3 T13: -0.0440 T23: -0.1993 REMARK 3 L TENSOR REMARK 3 L11: 5.0721 L22: 3.5655 REMARK 3 L33: 0.6887 L12: -2.4050 REMARK 3 L13: 0.5607 L23: 0.1047 REMARK 3 S TENSOR REMARK 3 S11: 0.3864 S12: 1.0063 S13: -1.1222 REMARK 3 S21: -0.4442 S22: -0.2176 S23: 0.2260 REMARK 3 S31: 0.1603 S32: 0.1613 S33: -0.1688 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 125 A 143 REMARK 3 ORIGIN FOR THE GROUP (A): -17.4590 8.7340 58.2650 REMARK 3 T TENSOR REMARK 3 T11: 0.1930 T22: 0.1098 REMARK 3 T33: 0.0681 T12: 0.0522 REMARK 3 T13: 0.0459 T23: 0.0164 REMARK 3 L TENSOR REMARK 3 L11: 13.4623 L22: 8.5097 REMARK 3 L33: 5.2180 L12: 4.9140 REMARK 3 L13: -3.7454 L23: -1.5164 REMARK 3 S TENSOR REMARK 3 S11: 0.2481 S12: -0.3635 S13: -0.1654 REMARK 3 S21: 0.5494 S22: -0.1405 S23: 0.5410 REMARK 3 S31: 0.2784 S32: -0.1862 S33: -0.1075 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 144 A 203 REMARK 3 ORIGIN FOR THE GROUP (A): -2.8790 -0.4190 50.2990 REMARK 3 T TENSOR REMARK 3 T11: 0.0970 T22: 0.0784 REMARK 3 T33: 0.1725 T12: 0.0029 REMARK 3 T13: -0.0163 T23: -0.0137 REMARK 3 L TENSOR REMARK 3 L11: 6.6300 L22: 3.8795 REMARK 3 L33: 1.6088 L12: -2.5464 REMARK 3 L13: 1.2840 L23: -1.2805 REMARK 3 S TENSOR REMARK 3 S11: 0.1392 S12: 0.0725 S13: -0.7230 REMARK 3 S21: -0.0259 S22: -0.1428 S23: -0.1694 REMARK 3 S31: 0.0810 S32: 0.2623 S33: 0.0036 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 204 A 296 REMARK 3 ORIGIN FOR THE GROUP (A): -13.1850 20.9410 57.3190 REMARK 3 T TENSOR REMARK 3 T11: 0.1364 T22: 0.0982 REMARK 3 T33: 0.0676 T12: 0.0200 REMARK 3 T13: -0.0134 T23: 0.0062 REMARK 3 L TENSOR REMARK 3 L11: 3.5293 L22: 2.4630 REMARK 3 L33: 3.0876 L12: -0.0500 REMARK 3 L13: -1.4598 L23: 0.5242 REMARK 3 S TENSOR REMARK 3 S11: 0.0465 S12: -0.3945 S13: 0.1860 REMARK 3 S21: 0.3163 S22: 0.0405 S23: 0.0730 REMARK 3 S31: -0.1569 S32: 0.0927 S33: -0.0871 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 45 B 75 REMARK 3 ORIGIN FOR THE GROUP (A): 16.9970 24.4930 35.4950 REMARK 3 T TENSOR REMARK 3 T11: 0.0419 T22: 0.0630 REMARK 3 T33: 0.0880 T12: -0.0004 REMARK 3 T13: -0.0311 T23: 0.0012 REMARK 3 L TENSOR REMARK 3 L11: 2.1746 L22: 3.8406 REMARK 3 L33: 10.0173 L12: 0.1645 REMARK 3 L13: -0.8662 L23: -4.0976 REMARK 3 S TENSOR REMARK 3 S11: -0.0192 S12: -0.1816 S13: 0.0497 REMARK 3 S21: 0.1265 S22: -0.2054 S23: -0.2363 REMARK 3 S31: -0.4009 S32: 0.5839 S33: 0.2245 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 76 B 116 REMARK 3 ORIGIN FOR THE GROUP (A): 5.7500 29.6030 29.0810 REMARK 3 T TENSOR REMARK 3 T11: 0.1157 T22: 0.0545 REMARK 3 T33: 0.1088 T12: 0.0668 REMARK 3 T13: -0.0018 T23: 0.0359 REMARK 3 L TENSOR REMARK 3 L11: 3.0707 L22: 2.7689 REMARK 3 L33: 8.8022 L12: 1.5728 REMARK 3 L13: -3.2819 L23: -2.8806 REMARK 3 S TENSOR REMARK 3 S11: 0.1208 S12: 0.2363 S13: 0.2977 REMARK 3 S21: -0.0888 S22: 0.0283 S23: 0.0804 REMARK 3 S31: -0.3549 S32: -0.2709 S33: -0.1490 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 117 B 144 REMARK 3 ORIGIN FOR THE GROUP (A): 14.5340 13.3880 15.2540 REMARK 3 T TENSOR REMARK 3 T11: 0.1877 T22: 0.1385 REMARK 3 T33: 0.1328 T12: -0.0316 REMARK 3 T13: 0.0208 T23: -0.0618 REMARK 3 L TENSOR REMARK 3 L11: 10.3931 L22: 6.3825 REMARK 3 L33: 4.1561 L12: -0.3228 REMARK 3 L13: 0.3049 L23: -1.2559 REMARK 3 S TENSOR REMARK 3 S11: -0.2574 S12: 0.5040 S13: 0.0777 REMARK 3 S21: -0.2209 S22: 0.0324 S23: -0.5584 REMARK 3 S31: 0.1224 S32: 0.4144 S33: 0.2250 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 145 B 192 REMARK 3 ORIGIN FOR THE GROUP (A): 9.0190 19.9780 35.4410 REMARK 3 T TENSOR REMARK 3 T11: 0.0423 T22: 0.0361 REMARK 3 T33: 0.0656 T12: 0.0183 REMARK 3 T13: -0.0157 T23: 0.0127 REMARK 3 L TENSOR REMARK 3 L11: 3.9998 L22: 1.3265 REMARK 3 L33: 6.6225 L12: 1.1795 REMARK 3 L13: -0.8016 L23: -0.9528 REMARK 3 S TENSOR REMARK 3 S11: -0.0191 S12: -0.2939 S13: -0.2269 REMARK 3 S21: -0.0143 S22: -0.0813 S23: 0.0239 REMARK 3 S31: 0.0994 S32: -0.0982 S33: 0.1004 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 193 B 237 REMARK 3 ORIGIN FOR THE GROUP (A): 3.2070 8.9470 18.7770 REMARK 3 T TENSOR REMARK 3 T11: 0.1425 T22: 0.1131 REMARK 3 T33: 0.0988 T12: -0.0911 REMARK 3 T13: 0.0192 T23: -0.0199 REMARK 3 L TENSOR REMARK 3 L11: 4.9459 L22: 5.5008 REMARK 3 L33: 5.8833 L12: -1.1351 REMARK 3 L13: 0.0177 L23: -0.0642 REMARK 3 S TENSOR REMARK 3 S11: -0.3355 S12: -0.0861 S13: -0.2082 REMARK 3 S21: 0.1478 S22: 0.2402 S23: 0.2307 REMARK 3 S31: 0.2388 S32: -0.4449 S33: 0.0953 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 238 B 296 REMARK 3 ORIGIN FOR THE GROUP (A): 12.2960 -0.3900 12.5290 REMARK 3 T TENSOR REMARK 3 T11: 0.3327 T22: 0.1527 REMARK 3 T33: 0.2157 T12: -0.0185 REMARK 3 T13: 0.0429 T23: -0.0608 REMARK 3 L TENSOR REMARK 3 L11: 6.4681 L22: 3.3713 REMARK 3 L33: 1.4820 L12: -2.3675 REMARK 3 L13: 0.5261 L23: 0.3518 REMARK 3 S TENSOR REMARK 3 S11: -0.0604 S12: 0.3459 S13: -0.1393 REMARK 3 S21: -0.1700 S22: 0.0165 S23: -0.1875 REMARK 3 S31: 0.2117 S32: 0.1290 S33: 0.0440 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 U VALUES REMARK 4 REMARK 4 3ROP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-MAY-11. REMARK 100 THE DEPOSITION ID IS D_1000065190. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAY-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97908 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37381 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.940 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.33900 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: 1YH3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE PH4.0, 0.2M REMARK 280 AMMONIUM ACETATE, 3% ISOPROPANOL, 15% PEG 10000, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 GLU A 43 REMARK 465 PHE A 44 REMARK 465 GLU B 43 REMARK 465 PHE B 44 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 ARG A 247 CB CG CD NE CZ NH1 NH2 REMARK 470 ARG B 247 CB CG CD NE CZ NH1 NH2 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 318 O HOH B 362 2.12 REMARK 500 O LEU B 230 NH1 ARG B 269 2.13 REMARK 500 NE2 HIS A 205 O HOH A 349 2.18 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 ILE A 128 55.87 -146.86 REMARK 500 ASP A 202 -120.82 58.62 REMARK 500 ARG A 247 -54.07 96.28 REMARK 500 SER A 250 -42.55 -130.27 REMARK 500 SER B 95 -0.51 70.89 REMARK 500 ILE B 128 58.64 -140.15 REMARK 500 ASP B 179 -78.43 -107.81 REMARK 500 ASN B 182 58.74 -94.34 REMARK 500 ASP B 202 -121.13 60.07 REMARK 500 SER B 295 -107.23 -66.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE REAL LEAVING GROUP NICOTINAMIDE OF LIGAND 50A CAN NOT BE SEEN REMARK 600 IN THE STRUCTURE REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YH3 RELATED DB: PDB REMARK 900 NATIVE FORM REMARK 900 RELATED ID: 3ROK RELATED DB: PDB REMARK 900 RELATED ID: 3ROM RELATED DB: PDB REMARK 900 RELATED ID: 3ROQ RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 Q -> T AT THIS POSITION IN GENBANK AAA68482 DBREF 3ROP A 45 296 UNP P28907 CD38_HUMAN 45 296 DBREF 3ROP B 45 296 UNP P28907 CD38_HUMAN 45 296 SEQADV 3ROP GLU A 43 UNP P28907 EXPRESSION TAG SEQADV 3ROP PHE A 44 UNP P28907 EXPRESSION TAG SEQADV 3ROP THR A 49 UNP P28907 GLN 49 SEE REMARK 999 SEQADV 3ROP ASP A 100 UNP P28907 ASN 100 ENGINEERED MUTATION SEQADV 3ROP ASP A 164 UNP P28907 ASN 164 ENGINEERED MUTATION SEQADV 3ROP ASP A 209 UNP P28907 ASN 209 ENGINEERED MUTATION SEQADV 3ROP ASP A 219 UNP P28907 ASN 219 ENGINEERED MUTATION SEQADV 3ROP GLU B 43 UNP P28907 EXPRESSION TAG SEQADV 3ROP PHE B 44 UNP P28907 EXPRESSION TAG SEQADV 3ROP THR B 49 UNP P28907 GLN 49 SEE REMARK 999 SEQADV 3ROP ASP B 100 UNP P28907 ASN 100 ENGINEERED MUTATION SEQADV 3ROP ASP B 164 UNP P28907 ASN 164 ENGINEERED MUTATION SEQADV 3ROP ASP B 209 UNP P28907 ASN 209 ENGINEERED MUTATION SEQADV 3ROP ASP B 219 UNP P28907 ASN 219 ENGINEERED MUTATION SEQRES 1 A 254 GLU PHE ARG TRP ARG GLN THR TRP SER GLY PRO GLY THR SEQRES 2 A 254 THR LYS ARG PHE PRO GLU THR VAL LEU ALA ARG CYS VAL SEQRES 3 A 254 LYS TYR THR GLU ILE HIS PRO GLU MET ARG HIS VAL ASP SEQRES 4 A 254 CYS GLN SER VAL TRP ASP ALA PHE LYS GLY ALA PHE ILE SEQRES 5 A 254 SER LYS HIS PRO CYS ASP ILE THR GLU GLU ASP TYR GLN SEQRES 6 A 254 PRO LEU MET LYS LEU GLY THR GLN THR VAL PRO CYS ASN SEQRES 7 A 254 LYS ILE LEU LEU TRP SER ARG ILE LYS ASP LEU ALA HIS SEQRES 8 A 254 GLN PHE THR GLN VAL GLN ARG ASP MET PHE THR LEU GLU SEQRES 9 A 254 ASP THR LEU LEU GLY TYR LEU ALA ASP ASP LEU THR TRP SEQRES 10 A 254 CYS GLY GLU PHE ASP THR SER LYS ILE ASN TYR GLN SER SEQRES 11 A 254 CYS PRO ASP TRP ARG LYS ASP CYS SER ASN ASN PRO VAL SEQRES 12 A 254 SER VAL PHE TRP LYS THR VAL SER ARG ARG PHE ALA GLU SEQRES 13 A 254 ALA ALA CYS ASP VAL VAL HIS VAL MET LEU ASP GLY SER SEQRES 14 A 254 ARG SER LYS ILE PHE ASP LYS ASP SER THR PHE GLY SER SEQRES 15 A 254 VAL GLU VAL HIS ASN LEU GLN PRO GLU LYS VAL GLN THR SEQRES 16 A 254 LEU GLU ALA TRP VAL ILE HIS GLY GLY ARG GLU ASP SER SEQRES 17 A 254 ARG ASP LEU CYS GLN ASP PRO THR ILE LYS GLU LEU GLU SEQRES 18 A 254 SER ILE ILE SER LYS ARG ASN ILE GLN PHE SER CYS LYS SEQRES 19 A 254 ASN ILE TYR ARG PRO ASP LYS PHE LEU GLN CYS VAL LYS SEQRES 20 A 254 ASN PRO GLU ASP SER SER CYS SEQRES 1 B 254 GLU PHE ARG TRP ARG GLN THR TRP SER GLY PRO GLY THR SEQRES 2 B 254 THR LYS ARG PHE PRO GLU THR VAL LEU ALA ARG CYS VAL SEQRES 3 B 254 LYS TYR THR GLU ILE HIS PRO GLU MET ARG HIS VAL ASP SEQRES 4 B 254 CYS GLN SER VAL TRP ASP ALA PHE LYS GLY ALA PHE ILE SEQRES 5 B 254 SER LYS HIS PRO CYS ASP ILE THR GLU GLU ASP TYR GLN SEQRES 6 B 254 PRO LEU MET LYS LEU GLY THR GLN THR VAL PRO CYS ASN SEQRES 7 B 254 LYS ILE LEU LEU TRP SER ARG ILE LYS ASP LEU ALA HIS SEQRES 8 B 254 GLN PHE THR GLN VAL GLN ARG ASP MET PHE THR LEU GLU SEQRES 9 B 254 ASP THR LEU LEU GLY TYR LEU ALA ASP ASP LEU THR TRP SEQRES 10 B 254 CYS GLY GLU PHE ASP THR SER LYS ILE ASN TYR GLN SER SEQRES 11 B 254 CYS PRO ASP TRP ARG LYS ASP CYS SER ASN ASN PRO VAL SEQRES 12 B 254 SER VAL PHE TRP LYS THR VAL SER ARG ARG PHE ALA GLU SEQRES 13 B 254 ALA ALA CYS ASP VAL VAL HIS VAL MET LEU ASP GLY SER SEQRES 14 B 254 ARG SER LYS ILE PHE ASP LYS ASP SER THR PHE GLY SER SEQRES 15 B 254 VAL GLU VAL HIS ASN LEU GLN PRO GLU LYS VAL GLN THR SEQRES 16 B 254 LEU GLU ALA TRP VAL ILE HIS GLY GLY ARG GLU ASP SER SEQRES 17 B 254 ARG ASP LEU CYS GLN ASP PRO THR ILE LYS GLU LEU GLU SEQRES 18 B 254 SER ILE ILE SER LYS ARG ASN ILE GLN PHE SER CYS LYS SEQRES 19 B 254 ASN ILE TYR ARG PRO ASP LYS PHE LEU GLN CYS VAL LYS SEQRES 20 B 254 ASN PRO GLU ASP SER SER CYS HET 50A A 301 13 HET NCA A 302 9 HET 50A B 301 13 HET NCA B 302 9 HETNAM 50A 2-DEOXY-2-FLUORO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE HETNAM NCA NICOTINAMIDE HETSYN 50A INHIBITOR CZ-50B ARABINOSYL-2-FLUORO-2- HETSYN 2 50A DEOXYNICOTINAMIDE MONONUCLEOTIDE, BOUND FORM; 2-DEOXY- HETSYN 3 50A 2-FLUORO-5-O-PHOSPHONO-ALPHA-D-RIBOSE; 2-DEOXY-2- HETSYN 4 50A FLUORO-5-O-PHOSPHONO-D-RIBOSE; 2-DEOXY-2-FLUORO-5-O- HETSYN 5 50A PHOSPHONO-RIBOSE FORMUL 3 50A 2(C5 H10 F O7 P) FORMUL 4 NCA 2(C6 H6 N2 O) FORMUL 7 HOH *266(H2 O) HELIX 1 1 ARG A 58 HIS A 74 1 17 HELIX 2 2 PRO A 75 ARG A 78 5 4 HELIX 3 3 ASP A 81 ILE A 94 1 14 HELIX 4 4 THR A 102 ASP A 105 5 4 HELIX 5 5 TYR A 106 GLY A 113 1 8 HELIX 6 6 ILE A 128 GLN A 139 1 12 HELIX 7 7 THR A 144 ASP A 147 5 4 HELIX 8 8 THR A 148 ASP A 155 1 8 HELIX 9 9 ASN A 183 ALA A 200 1 18 HELIX 10 10 SER A 220 VAL A 225 1 6 HELIX 11 11 VAL A 225 LEU A 230 1 6 HELIX 12 12 ASP A 252 GLN A 255 5 4 HELIX 13 13 ASP A 256 ARG A 269 1 14 HELIX 14 14 ARG A 280 ASN A 290 1 11 HELIX 15 15 ARG B 58 HIS B 74 1 17 HELIX 16 16 PRO B 75 ARG B 78 5 4 HELIX 17 17 ASP B 81 ILE B 94 1 14 HELIX 18 18 THR B 102 ASP B 105 5 4 HELIX 19 19 TYR B 106 GLY B 113 1 8 HELIX 20 20 ILE B 128 GLN B 139 1 12 HELIX 21 21 THR B 144 ASP B 147 5 4 HELIX 22 22 THR B 148 ASP B 155 1 8 HELIX 23 23 ASN B 183 ALA B 200 1 18 HELIX 24 24 SER B 220 VAL B 225 1 6 HELIX 25 25 GLU B 226 LEU B 230 5 5 HELIX 26 26 ASP B 252 GLN B 255 5 4 HELIX 27 27 ASP B 256 ARG B 269 1 14 HELIX 28 28 ARG B 280 ASN B 290 1 11 SHEET 1 A 2 GLY A 52 PRO A 53 0 SHEET 2 A 2 SER A 172 CYS A 173 -1 O CYS A 173 N GLY A 52 SHEET 1 B 4 LEU A 123 SER A 126 0 SHEET 2 B 4 ASP A 202 ASP A 209 1 O HIS A 205 N LEU A 124 SHEET 3 B 4 VAL A 235 ILE A 243 1 O TRP A 241 N VAL A 206 SHEET 4 B 4 GLN A 272 ILE A 278 1 O ILE A 278 N VAL A 242 SHEET 1 C 2 GLY A 161 GLU A 162 0 SHEET 2 C 2 THR A 165 ILE A 168 -1 O THR A 165 N GLU A 162 SHEET 1 D 2 GLY B 52 PRO B 53 0 SHEET 2 D 2 SER B 172 CYS B 173 -1 O CYS B 173 N GLY B 52 SHEET 1 E 4 LEU B 123 SER B 126 0 SHEET 2 E 4 ASP B 202 ASP B 209 1 O HIS B 205 N LEU B 124 SHEET 3 E 4 VAL B 235 ILE B 243 1 O TRP B 241 N VAL B 206 SHEET 4 E 4 GLN B 272 ILE B 278 1 O LYS B 276 N VAL B 242 SSBOND 1 CYS A 67 CYS A 82 1555 1555 2.95 SSBOND 2 CYS A 99 CYS A 180 1555 1555 2.05 SSBOND 3 CYS A 119 CYS A 201 1555 1555 2.05 SSBOND 4 CYS A 160 CYS A 173 1555 1555 2.05 SSBOND 5 CYS A 254 CYS A 275 1555 1555 2.10 SSBOND 6 CYS A 287 CYS A 296 1555 1555 2.01 SSBOND 7 CYS B 67 CYS B 82 1555 1555 2.08 SSBOND 8 CYS B 99 CYS B 180 1555 1555 2.08 SSBOND 9 CYS B 119 CYS B 201 1555 1555 2.06 SSBOND 10 CYS B 160 CYS B 173 1555 1555 2.10 SSBOND 11 CYS B 254 CYS B 275 1555 1555 2.04 SSBOND 12 CYS B 287 CYS B 296 1555 1555 2.04 LINK OE2 GLU A 226 C1 50A A 301 1555 1555 1.41 LINK OE2 GLU B 226 C1 50A B 301 1555 1555 1.37 CRYST1 41.817 53.630 63.540 109.72 91.19 94.81 P 1 2 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 0.023914 0.002012 0.001257 0.00000 SCALE2 0.000000 0.018712 0.006775 0.00000 SCALE3 0.000000 0.000000 0.016742 0.00000