HEADER HYDROLASE 10-MAY-12 4F46 TITLE CRYSTAL STRUCTURE OF WILD TYPE HUMAN CD38 IN COMPLEX WITH NAADP AND TITLE 2 ADPRP COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADP-RIBOSYL CYCLASE 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 46-300; 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, NAADP, CALCIUM SIGNALING, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.ZHANG,H.C.LEE,Q.HAO REVDAT 2 08-NOV-23 4F46 1 REMARK SEQADV REVDAT 1 03-APR-13 4F46 0 JRNL AUTH H.ZHANG,R.GRAEFF,H.C.LEE,Q.HAO JRNL TITL CRYSTAL STRUCTURES OF HUMAN CD38 IN COMPLEX WITH NAADP AND JRNL TITL 2 ADPRP JRNL REF MESSENGER V. 2 44 2013 JRNL REFN ISSN 2167-955X REMARK 2 REMARK 2 RESOLUTION. 1.69 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) : 1.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 53915 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2718 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) : 1.69 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2304 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 57.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.2250 REMARK 3 BIN FREE R VALUE SET COUNT : 127 REMARK 3 BIN FREE R VALUE : 0.2610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4058 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 392 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.03 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.12000 REMARK 3 B22 (A**2) : 0.40000 REMARK 3 B33 (A**2) : 1.02000 REMARK 3 B12 (A**2) : -0.06000 REMARK 3 B13 (A**2) : 0.08000 REMARK 3 B23 (A**2) : 0.45000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.108 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.102 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.065 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.825 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4268 ; 0.008 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2935 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5812 ; 1.209 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7117 ; 0.867 ; 3.012 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 506 ; 5.570 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 206 ;34.896 ;24.272 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 734 ;12.033 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;13.669 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 630 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4653 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 882 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 10 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 44 A 116 REMARK 3 ORIGIN FOR THE GROUP (A):-399.8000-918.4310 8.4910 REMARK 3 T TENSOR REMARK 3 T11: 0.0997 T22: 0.0232 REMARK 3 T33: 0.0728 T12: 0.0059 REMARK 3 T13: 0.0017 T23: -0.0178 REMARK 3 L TENSOR REMARK 3 L11: 2.1352 L22: 1.6905 REMARK 3 L33: 3.5417 L12: 0.1249 REMARK 3 L13: -0.5586 L23: -1.2439 REMARK 3 S TENSOR REMARK 3 S11: 0.0538 S12: -0.0208 S13: 0.1610 REMARK 3 S21: -0.0347 S22: -0.0462 S23: -0.0721 REMARK 3 S31: -0.2150 S32: 0.1096 S33: -0.0075 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 117 A 140 REMARK 3 ORIGIN FOR THE GROUP (A):-396.0990-932.8060 -7.7130 REMARK 3 T TENSOR REMARK 3 T11: 0.1404 T22: 0.1157 REMARK 3 T33: 0.1306 T12: -0.0204 REMARK 3 T13: 0.0030 T23: -0.0505 REMARK 3 L TENSOR REMARK 3 L11: 6.8586 L22: 5.2371 REMARK 3 L33: 5.8814 L12: -0.2498 REMARK 3 L13: 1.9958 L23: -1.2799 REMARK 3 S TENSOR REMARK 3 S11: -0.1199 S12: 0.2539 S13: -0.1074 REMARK 3 S21: 0.0599 S22: -0.0307 S23: -0.5635 REMARK 3 S31: 0.0622 S32: 0.4461 S33: 0.1505 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 141 A 193 REMARK 3 ORIGIN FOR THE GROUP (A):-401.5220-926.0370 9.7230 REMARK 3 T TENSOR REMARK 3 T11: 0.0272 T22: 0.0168 REMARK 3 T33: 0.0536 T12: 0.0114 REMARK 3 T13: -0.0102 T23: 0.0069 REMARK 3 L TENSOR REMARK 3 L11: 3.0833 L22: 1.3035 REMARK 3 L33: 6.1528 L12: 0.4185 REMARK 3 L13: -0.6226 L23: -0.3124 REMARK 3 S TENSOR REMARK 3 S11: -0.0413 S12: -0.1261 S13: -0.1232 REMARK 3 S21: -0.0361 S22: -0.0096 S23: 0.0277 REMARK 3 S31: 0.1495 S32: -0.1020 S33: 0.0510 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 194 A 233 REMARK 3 ORIGIN FOR THE GROUP (A):-407.3470-937.1380 -3.7400 REMARK 3 T TENSOR REMARK 3 T11: 0.1614 T22: 0.1252 REMARK 3 T33: 0.1027 T12: -0.0496 REMARK 3 T13: 0.0105 T23: -0.0205 REMARK 3 L TENSOR REMARK 3 L11: 5.7006 L22: 4.5937 REMARK 3 L33: 3.2814 L12: -0.7587 REMARK 3 L13: -0.2040 L23: -0.1170 REMARK 3 S TENSOR REMARK 3 S11: -0.2063 S12: -0.3467 S13: -0.3074 REMARK 3 S21: 0.3582 S22: 0.1639 S23: 0.1420 REMARK 3 S31: 0.1486 S32: -0.2738 S33: 0.0423 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 234 A 291 REMARK 3 ORIGIN FOR THE GROUP (A):-400.0440-945.7600 -10.2270 REMARK 3 T TENSOR REMARK 3 T11: 0.2484 T22: 0.1512 REMARK 3 T33: 0.1699 T12: -0.0227 REMARK 3 T13: 0.0413 T23: -0.0497 REMARK 3 L TENSOR REMARK 3 L11: 5.1397 L22: 2.4564 REMARK 3 L33: 1.1442 L12: -2.5957 REMARK 3 L13: 0.1666 L23: 0.0405 REMARK 3 S TENSOR REMARK 3 S11: -0.0652 S12: 0.1360 S13: -0.2202 REMARK 3 S21: -0.0232 S22: -0.0251 S23: -0.0074 REMARK 3 S31: 0.1719 S32: 0.0532 S33: 0.0904 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 : B 45 B 123 REMARK 3 ORIGIN FOR THE GROUP (A):-418.4270-952.3410 24.6090 REMARK 3 T TENSOR REMARK 3 T11: 0.1490 T22: 0.1597 REMARK 3 T33: 0.3474 T12: 0.0064 REMARK 3 T13: -0.0589 T23: -0.0303 REMARK 3 L TENSOR REMARK 3 L11: 3.8285 L22: 2.4726 REMARK 3 L33: 0.4697 L12: -1.4705 REMARK 3 L13: 0.1935 L23: -0.0057 REMARK 3 S TENSOR REMARK 3 S11: 0.2085 S12: 0.2240 S13: -1.0172 REMARK 3 S21: -0.0719 S22: -0.0846 S23: 0.1667 REMARK 3 S31: 0.1496 S32: 0.0465 S33: -0.1240 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 124 B 145 REMARK 3 ORIGIN FOR THE GROUP (A):-428.1630-937.4240 33.9620 REMARK 3 T TENSOR REMARK 3 T11: 0.1721 T22: 0.0736 REMARK 3 T33: 0.0873 T12: 0.0196 REMARK 3 T13: 0.0298 T23: 0.0335 REMARK 3 L TENSOR REMARK 3 L11: 7.6760 L22: 8.6064 REMARK 3 L33: 6.2432 L12: 3.8184 REMARK 3 L13: -3.3920 L23: 0.1921 REMARK 3 S TENSOR REMARK 3 S11: 0.1147 S12: -0.3938 S13: -0.0498 REMARK 3 S21: 0.7379 S22: -0.1391 S23: 0.4813 REMARK 3 S31: 0.2746 S32: -0.1847 S33: 0.0243 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 146 B 178 REMARK 3 ORIGIN FOR THE GROUP (A):-411.4780-951.5720 29.2680 REMARK 3 T TENSOR REMARK 3 T11: 0.1378 T22: 0.1171 REMARK 3 T33: 0.2752 T12: -0.0059 REMARK 3 T13: -0.0654 T23: 0.0623 REMARK 3 L TENSOR REMARK 3 L11: 13.8985 L22: 1.4839 REMARK 3 L33: 2.0184 L12: -1.6211 REMARK 3 L13: 1.5358 L23: -1.1328 REMARK 3 S TENSOR REMARK 3 S11: 0.2455 S12: -0.2470 S13: -1.3317 REMARK 3 S21: 0.0693 S22: -0.1834 S23: -0.0913 REMARK 3 S31: 0.1060 S32: 0.3350 S33: -0.0620 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 179 B 203 REMARK 3 ORIGIN FOR THE GROUP (A):-416.3710-940.1170 22.5250 REMARK 3 T TENSOR REMARK 3 T11: 0.0654 T22: 0.0865 REMARK 3 T33: 0.0592 T12: -0.0058 REMARK 3 T13: 0.0028 T23: -0.0024 REMARK 3 L TENSOR REMARK 3 L11: 8.8212 L22: 7.7281 REMARK 3 L33: 1.2982 L12: -7.6313 REMARK 3 L13: 1.9526 L23: -2.1657 REMARK 3 S TENSOR REMARK 3 S11: 0.2591 S12: 0.4647 S13: -0.1450 REMARK 3 S21: -0.2624 S22: -0.2859 S23: -0.0374 REMARK 3 S31: 0.1077 S32: 0.1774 S33: 0.0269 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 204 B 296 REMARK 3 ORIGIN FOR THE GROUP (A):-424.0790-925.0930 33.6200 REMARK 3 T TENSOR REMARK 3 T11: 0.1292 T22: 0.1006 REMARK 3 T33: 0.0591 T12: -0.0045 REMARK 3 T13: -0.0021 T23: -0.0009 REMARK 3 L TENSOR REMARK 3 L11: 2.5739 L22: 2.1612 REMARK 3 L33: 3.9132 L12: -0.1327 REMARK 3 L13: -1.6130 L23: 0.0749 REMARK 3 S TENSOR REMARK 3 S11: 0.0234 S12: -0.2591 S13: 0.1188 REMARK 3 S21: 0.3117 S22: 0.0160 S23: 0.0570 REMARK 3 S31: -0.1575 S32: 0.1159 S33: -0.0394 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 : 1.20 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 4F46 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000072432. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-SEP-09 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) : 0.97623 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MX225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53940 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.21300 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 (%): 44.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE PH 4.0, 15% PEG REMARK 280 10K, 0.2M AMMONIUM ACETATE, 3% ISOPROPANOL, 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 292 REMARK 465 ASP A 293 REMARK 465 SER A 294 REMARK 465 SER A 295 REMARK 465 CYS A 296 REMARK 465 THR A 297 REMARK 465 SER A 298 REMARK 465 GLU A 299 REMARK 465 ILE A 300 REMARK 465 GLU B 44 REMARK 465 THR B 297 REMARK 465 SER B 298 REMARK 465 GLU B 299 REMARK 465 ILE B 300 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 44 CG CD OE1 OE2 REMARK 470 ARG B 78 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 247 CG CD NE CZ NH1 NH2 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 SER A 95 -1.63 74.53 REMARK 500 ILE A 128 48.34 -152.36 REMARK 500 ASP A 179 -77.35 -107.01 REMARK 500 ASN A 182 59.61 -90.60 REMARK 500 ASP A 202 -120.88 61.71 REMARK 500 ILE B 128 48.16 -151.12 REMARK 500 ASP B 179 -65.16 -123.78 REMARK 500 CYS B 180 145.52 -170.82 REMARK 500 ASP B 202 -120.99 59.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 DN4 B 401 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DVN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DN4 B 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4F45 RELATED DB: PDB REMARK 900 CD38 E226Q MUTANT IN COMPLEX WITH NAADP DBREF 4F46 A 46 300 UNP P28907 CD38_HUMAN 46 300 DBREF 4F46 B 46 300 UNP P28907 CD38_HUMAN 46 300 SEQADV 4F46 GLU A 44 UNP P28907 EXPRESSION TAG SEQADV 4F46 PHE A 45 UNP P28907 EXPRESSION TAG SEQADV 4F46 THR A 49 UNP P28907 GLN 49 ENGINEERED MUTATION SEQADV 4F46 ASP A 100 UNP P28907 ASN 100 ENGINEERED MUTATION SEQADV 4F46 ASP A 164 UNP P28907 ASN 164 ENGINEERED MUTATION SEQADV 4F46 ASP A 209 UNP P28907 ASN 209 ENGINEERED MUTATION SEQADV 4F46 ASP A 219 UNP P28907 ASN 219 ENGINEERED MUTATION SEQADV 4F46 GLU B 44 UNP P28907 EXPRESSION TAG SEQADV 4F46 PHE B 45 UNP P28907 EXPRESSION TAG SEQADV 4F46 THR B 49 UNP P28907 GLN 49 ENGINEERED MUTATION SEQADV 4F46 ASP B 100 UNP P28907 ASN 100 ENGINEERED MUTATION SEQADV 4F46 ASP B 164 UNP P28907 ASN 164 ENGINEERED MUTATION SEQADV 4F46 ASP B 209 UNP P28907 ASN 209 ENGINEERED MUTATION SEQADV 4F46 ASP B 219 UNP P28907 ASN 219 ENGINEERED MUTATION SEQRES 1 A 257 GLU PHE TRP ARG GLN THR TRP SER GLY PRO GLY THR THR SEQRES 2 A 257 LYS ARG PHE PRO GLU THR VAL LEU ALA ARG CYS VAL LYS SEQRES 3 A 257 TYR THR GLU ILE HIS PRO GLU MET ARG HIS VAL ASP CYS SEQRES 4 A 257 GLN SER VAL TRP ASP ALA PHE LYS GLY ALA PHE ILE SER SEQRES 5 A 257 LYS HIS PRO CYS ASP ILE THR GLU GLU ASP TYR GLN PRO SEQRES 6 A 257 LEU MET LYS LEU GLY THR GLN THR VAL PRO CYS ASN LYS SEQRES 7 A 257 ILE LEU LEU TRP SER ARG ILE LYS ASP LEU ALA HIS GLN SEQRES 8 A 257 PHE THR GLN VAL GLN ARG ASP MET PHE THR LEU GLU ASP SEQRES 9 A 257 THR LEU LEU GLY TYR LEU ALA ASP ASP LEU THR TRP CYS SEQRES 10 A 257 GLY GLU PHE ASP THR SER LYS ILE ASN TYR GLN SER CYS SEQRES 11 A 257 PRO ASP TRP ARG LYS ASP CYS SER ASN ASN PRO VAL SER SEQRES 12 A 257 VAL PHE TRP LYS THR VAL SER ARG ARG PHE ALA GLU ALA SEQRES 13 A 257 ALA CYS ASP VAL VAL HIS VAL MET LEU ASP GLY SER ARG SEQRES 14 A 257 SER LYS ILE PHE ASP LYS ASP SER THR PHE GLY SER VAL SEQRES 15 A 257 GLU VAL HIS ASN LEU GLN PRO GLU LYS VAL GLN THR LEU SEQRES 16 A 257 GLU ALA TRP VAL ILE HIS GLY GLY ARG GLU ASP SER ARG SEQRES 17 A 257 ASP LEU CYS GLN ASP PRO THR ILE LYS GLU LEU GLU SER SEQRES 18 A 257 ILE ILE SER LYS ARG ASN ILE GLN PHE SER CYS LYS ASN SEQRES 19 A 257 ILE TYR ARG PRO ASP LYS PHE LEU GLN CYS VAL LYS ASN SEQRES 20 A 257 PRO GLU ASP SER SER CYS THR SER GLU ILE SEQRES 1 B 257 GLU PHE TRP ARG GLN THR TRP SER GLY PRO GLY THR THR SEQRES 2 B 257 LYS ARG PHE PRO GLU THR VAL LEU ALA ARG CYS VAL LYS SEQRES 3 B 257 TYR THR GLU ILE HIS PRO GLU MET ARG HIS VAL ASP CYS SEQRES 4 B 257 GLN SER VAL TRP ASP ALA PHE LYS GLY ALA PHE ILE SER SEQRES 5 B 257 LYS HIS PRO CYS ASP ILE THR GLU GLU ASP TYR GLN PRO SEQRES 6 B 257 LEU MET LYS LEU GLY THR GLN THR VAL PRO CYS ASN LYS SEQRES 7 B 257 ILE LEU LEU TRP SER ARG ILE LYS ASP LEU ALA HIS GLN SEQRES 8 B 257 PHE THR GLN VAL GLN ARG ASP MET PHE THR LEU GLU ASP SEQRES 9 B 257 THR LEU LEU GLY TYR LEU ALA ASP ASP LEU THR TRP CYS SEQRES 10 B 257 GLY GLU PHE ASP THR SER LYS ILE ASN TYR GLN SER CYS SEQRES 11 B 257 PRO ASP TRP ARG LYS ASP CYS SER ASN ASN PRO VAL SER SEQRES 12 B 257 VAL PHE TRP LYS THR VAL SER ARG ARG PHE ALA GLU ALA SEQRES 13 B 257 ALA CYS ASP VAL VAL HIS VAL MET LEU ASP GLY SER ARG SEQRES 14 B 257 SER LYS ILE PHE ASP LYS ASP SER THR PHE GLY SER VAL SEQRES 15 B 257 GLU VAL HIS ASN LEU GLN PRO GLU LYS VAL GLN THR LEU SEQRES 16 B 257 GLU ALA TRP VAL ILE HIS GLY GLY ARG GLU ASP SER ARG SEQRES 17 B 257 ASP LEU CYS GLN ASP PRO THR ILE LYS GLU LEU GLU SER SEQRES 18 B 257 ILE ILE SER LYS ARG ASN ILE GLN PHE SER CYS LYS ASN SEQRES 19 B 257 ILE TYR ARG PRO ASP LYS PHE LEU GLN CYS VAL LYS ASN SEQRES 20 B 257 PRO GLU ASP SER SER CYS THR SER GLU ILE HET DVN A 401 40 HET DN4 B 401 26 HETNAM DVN [[(2R,3R,4R,5R)-5-(6-AMINOPURIN-9-YL)-3-OXIDANYL-4- HETNAM 2 DVN PHOSPHONOOXY-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] HETNAM 3 DVN [(2R,3S,4R,5S)-3,4,5-TRIS(OXIDANYL)OXOLAN-2-YL]METHYL HETNAM 4 DVN HYDROGEN PHOSPHATE HETNAM DN4 [[(2R,3R,4R,5R)-5-(6-AMINOPURIN-9-YL)-3-OXIDANYL-4- HETNAM 2 DN4 PHOSPHONOOXY-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] HETNAM 3 DN4 [(2R,3S,4R,5R)-5-(3-CARBOXYPYRIDIN-1-IUM-1-YL)-3,4- HETNAM 4 DN4 BIS(OXIDANYL)OXOLAN-2-YL]METHYL PHOSPHATE HETSYN DN4 NICOTINIC ACID ADENINE DINUCLEOTIDE PHOSPHATE FORMUL 3 DVN C15 H24 N5 O17 P3 FORMUL 4 DN4 C21 H27 N6 O18 P3 FORMUL 5 HOH *392(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 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 VAL B 225 LEU B 230 1 6 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 ILE A 243 N LEU A 208 SHEET 4 B 4 GLN A 272 ILE A 278 1 O LYS A 276 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 TRP B 241 N VAL B 206 SHEET 4 D 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 2.09 SSBOND 2 CYS A 99 CYS A 180 1555 1555 2.04 SSBOND 3 CYS A 119 CYS A 201 1555 1555 2.04 SSBOND 4 CYS A 160 CYS A 173 1555 1555 2.07 SSBOND 5 CYS A 254 CYS A 275 1555 1555 2.05 SSBOND 6 CYS B 67 CYS B 82 1555 1555 2.06 SSBOND 7 CYS B 99 CYS B 180 1555 1555 2.04 SSBOND 8 CYS B 119 CYS B 201 1555 1555 2.05 SSBOND 9 CYS B 160 CYS B 173 1555 1555 2.03 SSBOND 10 CYS B 254 CYS B 275 1555 1555 2.07 SSBOND 11 CYS B 287 CYS B 296 1555 1555 1.99 SITE 1 AC1 20 TRP A 125 SER A 126 ARG A 127 LYS A 129 SITE 2 AC1 20 LEU A 145 GLU A 146 VAL A 185 TRP A 189 SITE 3 AC1 20 SER A 193 SER A 220 THR A 221 PHE A 222 SITE 4 AC1 20 GLU A 226 HOH A 506 HOH A 550 HOH A 614 SITE 5 AC1 20 HOH A 624 HOH A 682 HOH A 699 HOH A 700 SITE 1 AC2 16 LEU B 124 TRP B 125 SER B 126 ARG B 127 SITE 2 AC2 16 LYS B 129 LEU B 145 GLU B 146 ASP B 155 SITE 3 AC2 16 TRP B 189 SER B 193 SER B 220 THR B 221 SITE 4 AC2 16 PHE B 222 GLU B 226 HOH B 504 HOH B 670 CRYST1 41.848 53.683 63.380 110.35 91.42 94.53 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 0.023896 0.001892 0.001342 0.00000 SCALE2 0.000000 0.018686 0.007001 0.00000 SCALE3 0.000000 0.000000 0.016854 0.00000