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 1 28-DEC-11 3ROP 0
JRNL AUTH A.K.KWONG,Z.CHEN,H.M.ZHANG,F.P.LEUNG,C.M.LAM,K.Y.TING,
JRNL AUTH 2 L.ZHANG,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 2011
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 5.5.0110
REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON
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 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1725 ; 1.815 ; 3.000
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1648 ; 2.912 ; 4.500
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 12-MAY-11.
REMARK 100 THE RCSB ID CODE IS RCSB065190.
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 : HKL
REMARK 200 DATA SCALING SOFTWARE : HKL
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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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 THE REAL LEAVING GROUP NICOTINAMIDE OF LIGAND 50A 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 50A A 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCA A 302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 50A B 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCA B 302
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 1,4-ANHYDRO-2-DEOXY-2-FLUORO-5-O-PHOSPHONO-D-RIBITOL
HETNAM NCA NICOTINAMIDE
FORMUL 3 50A 2(C5 H10 F O6 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 C1D 50A A 301 1555 1555 1.41
LINK OE2 GLU B 226 C1D 50A B 301 1555 1555 1.37
SITE 1 AC1 14 HOH A 5 LEU A 124 TRP A 125 SER A 126
SITE 2 AC1 14 ARG A 127 LEU A 145 SER A 193 SER A 220
SITE 3 AC1 14 THR A 221 PHE A 222 GLU A 226 NCA A 302
SITE 4 AC1 14 HOH A 402 HOH A 408
SITE 1 AC2 6 TRP A 125 GLU A 146 TRP A 189 THR A 221
SITE 2 AC2 6 50A A 301 HOH A 317
SITE 1 AC3 13 LEU B 124 TRP B 125 SER B 126 ARG B 127
SITE 2 AC3 13 LEU B 145 SER B 193 SER B 220 THR B 221
SITE 3 AC3 13 PHE B 222 GLU B 226 NCA B 302 HOH B 393
SITE 4 AC3 13 HOH B 409
SITE 1 AC4 3 GLU B 146 THR B 221 50A B 301
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
(ATOM LINES ARE NOT SHOWN.)
END
