HEADER HYDROLASE/HYDROLASE INHIBITOR 26-APR-11 3ROM TITLE CRYSTAL STRUCTURE OF HUMAN CD38 IN COMPLEX WITH COMPOUND CZ-48 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 48, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.ZHANG,H.C.LEE,Q.HAO REVDAT 4 01-NOV-23 3ROM 1 REMARK SEQADV HETSYN LINK REVDAT 3 08-NOV-17 3ROM 1 REMARK REVDAT 2 03-JUL-13 3ROM 1 JRNL HETNAM FORMUL HETATM REVDAT 2 2 1 HETSYN REVDAT 1 21-DEC-11 3ROM 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. 2.04 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) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 31515 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1583 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) : 2.04 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2016 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE SET COUNT : 88 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4089 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 237 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.42000 REMARK 3 B22 (A**2) : -0.52000 REMARK 3 B33 (A**2) : 0.53000 REMARK 3 B12 (A**2) : -0.28000 REMARK 3 B13 (A**2) : -0.67000 REMARK 3 B23 (A**2) : 0.75000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.182 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.129 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.363 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4232 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2910 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5742 ; 1.088 ; 1.941 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7053 ; 0.799 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 503 ; 5.305 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 205 ;36.145 ;24.146 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 734 ;13.155 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;14.892 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 621 ; 0.067 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4629 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 859 ; 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): 2527 ; 0.401 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1004 ; 0.096 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4118 ; 0.797 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1705 ; 1.429 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1624 ; 2.255 ; 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 100 REMARK 3 ORIGIN FOR THE GROUP (A): 4.3820 16.0250 2.0010 REMARK 3 T TENSOR REMARK 3 T11: 0.1906 T22: 0.0403 REMARK 3 T33: 0.4556 T12: 0.0287 REMARK 3 T13: 0.0162 T23: 0.0536 REMARK 3 L TENSOR REMARK 3 L11: 7.6309 L22: 4.3988 REMARK 3 L33: 2.9755 L12: 2.0667 REMARK 3 L13: -0.8322 L23: -1.1574 REMARK 3 S TENSOR REMARK 3 S11: 0.2628 S12: 0.2800 S13: 0.8463 REMARK 3 S21: -0.0038 S22: 0.1359 S23: 0.8578 REMARK 3 S31: -0.2194 S32: -0.1762 S33: -0.3986 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 101 A 126 REMARK 3 ORIGIN FOR THE GROUP (A): -0.6230 3.0910 9.4290 REMARK 3 T TENSOR REMARK 3 T11: 0.1639 T22: 0.1417 REMARK 3 T33: 0.2521 T12: 0.0069 REMARK 3 T13: 0.0384 T23: -0.0608 REMARK 3 L TENSOR REMARK 3 L11: 4.1857 L22: 6.4269 REMARK 3 L33: 0.4512 L12: 5.1401 REMARK 3 L13: 0.0802 L23: 0.3006 REMARK 3 S TENSOR REMARK 3 S11: 0.5510 S12: -0.3525 S13: 0.5131 REMARK 3 S21: 0.6346 S22: -0.4000 S23: 0.5363 REMARK 3 S31: -0.0867 S32: 0.0171 S33: -0.1511 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 127 A 154 REMARK 3 ORIGIN FOR THE GROUP (A): -7.0060 1.3580 -2.4240 REMARK 3 T TENSOR REMARK 3 T11: 0.2041 T22: 0.2501 REMARK 3 T33: 0.2567 T12: -0.0024 REMARK 3 T13: -0.0365 T23: 0.1549 REMARK 3 L TENSOR REMARK 3 L11: 5.6179 L22: 5.6066 REMARK 3 L33: 3.7461 L12: 0.5441 REMARK 3 L13: 3.0643 L23: 3.6822 REMARK 3 S TENSOR REMARK 3 S11: 0.1519 S12: 0.4308 S13: 0.3484 REMARK 3 S21: -0.3113 S22: -0.3800 S23: 0.1584 REMARK 3 S31: -0.0993 S32: -0.0664 S33: 0.2281 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 155 A 193 REMARK 3 ORIGIN FOR THE GROUP (A): 12.9410 10.1010 0.8910 REMARK 3 T TENSOR REMARK 3 T11: 0.1063 T22: 0.1163 REMARK 3 T33: 0.1652 T12: 0.0287 REMARK 3 T13: 0.0050 T23: -0.0037 REMARK 3 L TENSOR REMARK 3 L11: 4.4460 L22: 6.6806 REMARK 3 L33: 3.4703 L12: 2.5510 REMARK 3 L13: -1.7755 L23: -1.9238 REMARK 3 S TENSOR REMARK 3 S11: -0.0002 S12: 0.2201 S13: 0.0577 REMARK 3 S21: -0.3686 S22: -0.0155 S23: -0.3454 REMARK 3 S31: 0.0842 S32: 0.3034 S33: 0.0158 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 194 A 254 REMARK 3 ORIGIN FOR THE GROUP (A): 0.1070 -11.1540 0.0530 REMARK 3 T TENSOR REMARK 3 T11: 0.0746 T22: 0.0648 REMARK 3 T33: 0.0864 T12: 0.0255 REMARK 3 T13: 0.0092 T23: -0.0026 REMARK 3 L TENSOR REMARK 3 L11: 5.1409 L22: 3.2787 REMARK 3 L33: 5.9042 L12: 0.3207 REMARK 3 L13: -0.5170 L23: 0.7236 REMARK 3 S TENSOR REMARK 3 S11: -0.0043 S12: 0.4223 S13: 0.0231 REMARK 3 S21: -0.2444 S22: 0.0152 S23: -0.2109 REMARK 3 S31: -0.0368 S32: 0.2889 S33: -0.0109 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 255 A 296 REMARK 3 ORIGIN FOR THE GROUP (A): -6.6860 -15.1730 -5.1340 REMARK 3 T TENSOR REMARK 3 T11: 0.1509 T22: 0.2190 REMARK 3 T33: 0.1453 T12: -0.0207 REMARK 3 T13: 0.0141 T23: -0.0568 REMARK 3 L TENSOR REMARK 3 L11: 3.3549 L22: 3.0617 REMARK 3 L33: 2.7520 L12: -0.3444 REMARK 3 L13: 0.7070 L23: -0.1504 REMARK 3 S TENSOR REMARK 3 S11: 0.1317 S12: 0.4056 S13: -0.3826 REMARK 3 S21: -0.3448 S22: 0.0878 S23: 0.3657 REMARK 3 S31: 0.1523 S32: -0.2688 S33: -0.2196 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 44 B 79 REMARK 3 ORIGIN FOR THE GROUP (A): 27.0720 -19.8150 19.6470 REMARK 3 T TENSOR REMARK 3 T11: 0.0824 T22: 0.1070 REMARK 3 T33: 0.2304 T12: 0.0175 REMARK 3 T13: -0.0213 T23: 0.0195 REMARK 3 L TENSOR REMARK 3 L11: 4.4295 L22: 4.2764 REMARK 3 L33: 8.3021 L12: -0.2953 REMARK 3 L13: 0.7750 L23: -3.7765 REMARK 3 S TENSOR REMARK 3 S11: 0.0560 S12: -0.5022 S13: -0.5729 REMARK 3 S21: 0.1638 S22: -0.1234 S23: -0.2987 REMARK 3 S31: 0.4312 S32: 0.3249 S33: 0.0674 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 80 B 126 REMARK 3 ORIGIN FOR THE GROUP (A): 16.1730 -20.7490 25.5580 REMARK 3 T TENSOR REMARK 3 T11: 0.1829 T22: 0.2322 REMARK 3 T33: 0.1874 T12: -0.0385 REMARK 3 T13: -0.0193 T23: 0.0946 REMARK 3 L TENSOR REMARK 3 L11: 1.9951 L22: 1.3059 REMARK 3 L33: 4.2864 L12: 0.8270 REMARK 3 L13: 0.8353 L23: 1.0346 REMARK 3 S TENSOR REMARK 3 S11: 0.2042 S12: -0.5588 S13: -0.4716 REMARK 3 S21: 0.3474 S22: -0.1056 S23: -0.1389 REMARK 3 S31: 0.5232 S32: -0.3107 S33: -0.0986 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 127 B 150 REMARK 3 ORIGIN FOR THE GROUP (A): 26.2980 -10.5870 36.7830 REMARK 3 T TENSOR REMARK 3 T11: 0.2138 T22: 0.4296 REMARK 3 T33: 0.2291 T12: 0.0122 REMARK 3 T13: -0.0164 T23: 0.0566 REMARK 3 L TENSOR REMARK 3 L11: 5.2611 L22: 9.6440 REMARK 3 L33: 6.4006 L12: 3.4295 REMARK 3 L13: 3.3243 L23: 5.4882 REMARK 3 S TENSOR REMARK 3 S11: 0.0646 S12: -0.5102 S13: 0.0154 REMARK 3 S21: 0.6495 S22: 0.3568 S23: -0.4719 REMARK 3 S31: 0.0104 S32: 0.1687 S33: -0.4214 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 151 B 193 REMARK 3 ORIGIN FOR THE GROUP (A): 19.1270 -13.6380 16.1160 REMARK 3 T TENSOR REMARK 3 T11: 0.0261 T22: 0.0483 REMARK 3 T33: 0.0739 T12: 0.0034 REMARK 3 T13: -0.0082 T23: -0.0093 REMARK 3 L TENSOR REMARK 3 L11: 5.4591 L22: 2.3451 REMARK 3 L33: 4.0449 L12: 0.2026 REMARK 3 L13: 0.3867 L23: -0.3808 REMARK 3 S TENSOR REMARK 3 S11: 0.0348 S12: -0.1288 S13: -0.0005 REMARK 3 S21: -0.0439 S22: -0.0506 S23: -0.0207 REMARK 3 S31: -0.2092 S32: -0.1581 S33: 0.0158 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 194 B 244 REMARK 3 ORIGIN FOR THE GROUP (A): 14.0700 -3.5990 36.1060 REMARK 3 T TENSOR REMARK 3 T11: 0.2477 T22: 0.4146 REMARK 3 T33: 0.1119 T12: 0.0159 REMARK 3 T13: 0.0348 T23: -0.0471 REMARK 3 L TENSOR REMARK 3 L11: 5.5457 L22: 6.0754 REMARK 3 L33: 3.3163 L12: 2.6396 REMARK 3 L13: 1.8091 L23: 1.4793 REMARK 3 S TENSOR REMARK 3 S11: -0.0525 S12: 0.1837 S13: 0.2369 REMARK 3 S21: -0.3398 S22: -0.1909 S23: 0.2287 REMARK 3 S31: -0.0307 S32: -0.3901 S33: 0.2434 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 245 B 296 REMARK 3 ORIGIN FOR THE GROUP (A): 22.1100 4.7620 42.2550 REMARK 3 T TENSOR REMARK 3 T11: 0.3709 T22: 0.4379 REMARK 3 T33: 0.1551 T12: -0.0457 REMARK 3 T13: 0.0031 T23: -0.0533 REMARK 3 L TENSOR REMARK 3 L11: 4.9815 L22: 4.8605 REMARK 3 L33: 2.6405 L12: 0.7322 REMARK 3 L13: -0.1782 L23: -0.4517 REMARK 3 S TENSOR REMARK 3 S11: 0.0421 S12: -0.1105 S13: 0.4569 REMARK 3 S21: 0.2504 S22: -0.2499 S23: -0.3274 REMARK 3 S31: -0.1509 S32: 0.2014 S33: 0.2078 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 3ROM 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_1000065187. 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 : 31537 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 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 (%) : 97.9 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.38400 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 (%): 44.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 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 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 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 248 CG CD OE1 OE2 REMARK 470 PHE B 44 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG B 247 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 OE2 GLU A 103 NH1 ARG A 194 1.29 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 46.28 -147.20 REMARK 500 ASP A 179 -73.89 -116.43 REMARK 500 ASN A 182 54.96 -90.24 REMARK 500 ASP A 202 -123.35 61.48 REMARK 500 ARG B 127 7.60 57.74 REMARK 500 ASP B 179 -79.23 -112.71 REMARK 500 ASP B 202 -117.20 61.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE REAL LEAVING GROUP NICOTINAMIDE OF LIGAND 48Z CAN NOT BE SEEN REMARK 600 IN THE STRUCTURE REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 48Z A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 48Z B 301 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: 3ROP 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 3ROM A 45 296 UNP P28907 CD38_HUMAN 45 296 DBREF 3ROM B 45 296 UNP P28907 CD38_HUMAN 45 296 SEQADV 3ROM GLU A 43 UNP P28907 EXPRESSION TAG SEQADV 3ROM PHE A 44 UNP P28907 EXPRESSION TAG SEQADV 3ROM THR A 49 UNP P28907 GLN 49 SEE REMARK 999 SEQADV 3ROM ASP A 100 UNP P28907 ASN 100 ENGINEERED MUTATION SEQADV 3ROM ASP A 164 UNP P28907 ASN 164 ENGINEERED MUTATION SEQADV 3ROM ASP A 209 UNP P28907 ASN 209 ENGINEERED MUTATION SEQADV 3ROM ASP A 219 UNP P28907 ASN 219 ENGINEERED MUTATION SEQADV 3ROM GLU B 43 UNP P28907 EXPRESSION TAG SEQADV 3ROM PHE B 44 UNP P28907 EXPRESSION TAG SEQADV 3ROM THR B 49 UNP P28907 GLN 49 SEE REMARK 999 SEQADV 3ROM ASP B 100 UNP P28907 ASN 100 ENGINEERED MUTATION SEQADV 3ROM ASP B 164 UNP P28907 ASN 164 ENGINEERED MUTATION SEQADV 3ROM ASP B 209 UNP P28907 ASN 209 ENGINEERED MUTATION SEQADV 3ROM 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 48Z A 301 13 HET 48Z B 301 13 HETNAM 48Z 2-DEOXY-2-FLUORO-5-O-THIOPHOSPHONO-ALPHA-D- HETNAM 2 48Z ARABINOFURANOSE FORMUL 3 48Z 2(C5 H10 F O6 P S) FORMUL 5 HOH *237(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 GLU A 103 ASP A 105 5 3 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 GLU A 226 LEU A 230 5 5 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 LYS B 268 1 13 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 B 52 PRO B 53 0 SHEET 2 C 2 SER B 172 CYS B 173 -1 O CYS B 173 N GLY B 52 SHEET 1 D 4 LEU B 123 SER B 126 0 SHEET 2 D 4 ASP B 202 ASP B 209 1 O HIS B 205 N LEU B 124 SHEET 3 D 4 VAL B 235 ILE B 243 1 O GLU B 239 N VAL B 204 SHEET 4 D 4 GLN B 272 ILE B 278 1 O SER B 274 N ALA B 240 SSBOND 1 CYS A 67 CYS A 82 1555 1555 2.06 SSBOND 2 CYS A 99 CYS A 180 1555 1555 2.06 SSBOND 3 CYS A 119 CYS A 201 1555 1555 2.05 SSBOND 4 CYS A 160 CYS A 173 1555 1555 2.07 SSBOND 5 CYS A 254 CYS A 275 1555 1555 2.08 SSBOND 6 CYS A 287 CYS A 296 1555 1555 2.03 SSBOND 7 CYS B 67 CYS B 82 1555 1555 2.07 SSBOND 8 CYS B 99 CYS B 180 1555 1555 2.06 SSBOND 9 CYS B 119 CYS B 201 1555 1555 2.04 SSBOND 10 CYS B 160 CYS B 173 1555 1555 2.11 SSBOND 11 CYS B 254 CYS B 275 1555 1555 2.05 SSBOND 12 CYS B 287 CYS B 296 1555 1555 2.04 LINK OE2 GLU A 226 C1 48Z A 301 1555 1555 1.43 LINK OE2 GLU B 226 C1 48Z B 301 1555 1555 1.42 SITE 1 AC1 8 TRP A 125 SER A 126 ARG A 127 SER A 193 SITE 2 AC1 8 SER A 220 THR A 221 PHE A 222 GLU A 226 SITE 1 AC2 10 TRP B 125 SER B 126 ARG B 127 GLU B 146 SITE 2 AC2 10 SER B 193 SER B 220 THR B 221 PHE B 222 SITE 3 AC2 10 GLU B 226 HOH B 381 CRYST1 41.914 50.847 68.617 65.21 83.60 82.52 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 0.023858 -0.003131 -0.001524 0.00000 SCALE2 0.000000 0.019836 -0.008939 0.00000 SCALE3 0.000000 0.000000 0.016085 0.00000