HEADER HYDROLASE/HYDROLASE INHIBITOR 26-APR-11 3ROK TITLE CRYSTAL STRUCTURE OF HUMAN CD38 IN COMPLEX WITH COMPOUND CZ-27 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, CALCIUM SIGNALING, KEYWDS 2 INHIBITORY COMPOUND, COVALENT INTERMEDIATE, CZ-27, HYDROLASE- KEYWDS 3 HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.ZHANG,H.C.LEE,Q.HAO REVDAT 5 01-NOV-23 3ROK 1 HETSYN REVDAT 4 29-JUL-20 3ROK 1 REMARK SEQADV LINK SITE REVDAT 3 08-NOV-17 3ROK 1 REMARK REVDAT 2 03-JUL-13 3ROK 1 JRNL HETNAM FORMUL HETATM REVDAT 2 2 1 HETSYN REVDAT 1 21-DEC-11 3ROK 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. 1.65 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 59515 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) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3006 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3900 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.75 REMARK 3 BIN R VALUE (WORKING SET) : 0.2120 REMARK 3 BIN FREE R VALUE SET COUNT : 188 REMARK 3 BIN FREE R VALUE : 0.2240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4082 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 368 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.17000 REMARK 3 B22 (A**2) : 0.41000 REMARK 3 B33 (A**2) : 1.17000 REMARK 3 B12 (A**2) : -0.02000 REMARK 3 B13 (A**2) : 0.11000 REMARK 3 B23 (A**2) : 0.61000 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): 0.101 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.065 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.105 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4252 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2935 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5771 ; 1.282 ; 1.942 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7101 ; 0.816 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 507 ; 5.512 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 209 ;34.864 ;24.258 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 741 ;12.826 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;14.631 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 621 ; 0.138 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4652 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 860 ; 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): 2525 ; 0.574 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1003 ; 0.157 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4121 ; 1.145 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1727 ; 1.961 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1647 ; 3.022 ; 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 : 8 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 46 A 116 REMARK 3 ORIGIN FOR THE GROUP (A): -6.1050 -7.7260 48.6060 REMARK 3 T TENSOR REMARK 3 T11: 0.0955 T22: 0.0414 REMARK 3 T33: 0.3922 T12: 0.0379 REMARK 3 T13: -0.0628 T23: -0.0893 REMARK 3 L TENSOR REMARK 3 L11: 8.3697 L22: 2.7773 REMARK 3 L33: 1.9212 L12: 0.1430 REMARK 3 L13: 0.7480 L23: -0.3829 REMARK 3 S TENSOR REMARK 3 S11: 0.3269 S12: 0.3229 S13: -1.3866 REMARK 3 S21: -0.0829 S22: -0.0840 S23: 0.0764 REMARK 3 S31: 0.1261 S32: -0.0172 S33: -0.2430 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): -17.3950 9.7680 55.8980 REMARK 3 T TENSOR REMARK 3 T11: 0.1493 T22: 0.0678 REMARK 3 T33: 0.0693 T12: 0.0163 REMARK 3 T13: 0.0449 T23: 0.0448 REMARK 3 L TENSOR REMARK 3 L11: 7.3967 L22: 5.2422 REMARK 3 L33: 7.8238 L12: 0.3727 REMARK 3 L13: 3.6823 L23: -0.9900 REMARK 3 S TENSOR REMARK 3 S11: 0.2122 S12: -0.5307 S13: -0.5258 REMARK 3 S21: 0.6150 S22: 0.0068 S23: 0.2940 REMARK 3 S31: 0.4860 S32: -0.2091 S33: -0.2191 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): -1.9170 -1.7590 52.0360 REMARK 3 T TENSOR REMARK 3 T11: 0.0644 T22: 0.0390 REMARK 3 T33: 0.1544 T12: -0.0038 REMARK 3 T13: -0.0374 T23: 0.0087 REMARK 3 L TENSOR REMARK 3 L11: 11.6648 L22: 3.3027 REMARK 3 L33: 1.9921 L12: -1.6584 REMARK 3 L13: 1.4609 L23: -1.6749 REMARK 3 S TENSOR REMARK 3 S11: 0.2206 S12: -0.3850 S13: -0.8678 REMARK 3 S21: 0.1065 S22: -0.1026 S23: -0.1434 REMARK 3 S31: -0.0215 S32: 0.1175 S33: -0.1180 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 296 REMARK 3 ORIGIN FOR THE GROUP (A): -12.7500 20.1910 55.9950 REMARK 3 T TENSOR REMARK 3 T11: 0.1066 T22: 0.0764 REMARK 3 T33: 0.0178 T12: 0.0122 REMARK 3 T13: 0.0112 T23: 0.0045 REMARK 3 L TENSOR REMARK 3 L11: 3.2173 L22: 3.0502 REMARK 3 L33: 3.3911 L12: 0.3053 REMARK 3 L13: -0.4503 L23: 0.2172 REMARK 3 S TENSOR REMARK 3 S11: 0.0697 S12: -0.3631 S13: 0.1112 REMARK 3 S21: 0.4529 S22: -0.0224 S23: 0.0561 REMARK 3 S31: -0.1276 S32: 0.0235 S33: -0.0472 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 : B 45 B 116 REMARK 3 ORIGIN FOR THE GROUP (A): 11.1110 27.4770 31.8560 REMARK 3 T TENSOR REMARK 3 T11: 0.0775 T22: 0.0112 REMARK 3 T33: 0.0651 T12: 0.0042 REMARK 3 T13: 0.0031 T23: -0.0007 REMARK 3 L TENSOR REMARK 3 L11: 2.9164 L22: 2.0632 REMARK 3 L33: 4.1016 L12: 0.2611 REMARK 3 L13: -0.9255 L23: -1.2008 REMARK 3 S TENSOR REMARK 3 S11: 0.0359 S12: 0.0612 S13: 0.2457 REMARK 3 S21: -0.0735 S22: -0.0344 S23: -0.0574 REMARK 3 S31: -0.3071 S32: 0.1034 S33: -0.0015 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 117 B 144 REMARK 3 ORIGIN FOR THE GROUP (A): 14.5620 13.6050 15.1020 REMARK 3 T TENSOR REMARK 3 T11: 0.1887 T22: 0.1371 REMARK 3 T33: 0.1043 T12: -0.0227 REMARK 3 T13: 0.0120 T23: -0.0435 REMARK 3 L TENSOR REMARK 3 L11: 9.0569 L22: 5.1422 REMARK 3 L33: 3.4988 L12: 0.2589 REMARK 3 L13: 1.3936 L23: -0.2095 REMARK 3 S TENSOR REMARK 3 S11: -0.2496 S12: 0.5517 S13: 0.0705 REMARK 3 S21: -0.0650 S22: 0.1103 S23: -0.5878 REMARK 3 S31: -0.0449 S32: 0.4029 S33: 0.1394 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 145 B 193 REMARK 3 ORIGIN FOR THE GROUP (A): 9.2500 20.1520 35.1510 REMARK 3 T TENSOR REMARK 3 T11: 0.0196 T22: 0.0170 REMARK 3 T33: 0.0308 T12: 0.0086 REMARK 3 T13: -0.0005 T23: 0.0115 REMARK 3 L TENSOR REMARK 3 L11: 3.8014 L22: 1.2711 REMARK 3 L33: 6.4158 L12: 0.7406 REMARK 3 L13: -1.0490 L23: -1.0245 REMARK 3 S TENSOR REMARK 3 S11: -0.0817 S12: -0.1612 S13: -0.1550 REMARK 3 S21: -0.0789 S22: 0.0216 S23: 0.0190 REMARK 3 S31: 0.1713 S32: -0.0381 S33: 0.0600 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 194 B 296 REMARK 3 ORIGIN FOR THE GROUP (A): 8.5270 3.4740 15.1390 REMARK 3 T TENSOR REMARK 3 T11: 0.2522 T22: 0.1437 REMARK 3 T33: 0.1238 T12: -0.0560 REMARK 3 T13: 0.0245 T23: -0.0438 REMARK 3 L TENSOR REMARK 3 L11: 3.6389 L22: 4.8084 REMARK 3 L33: 2.0777 L12: -1.5181 REMARK 3 L13: -0.0879 L23: -0.1971 REMARK 3 S TENSOR REMARK 3 S11: -0.1659 S12: 0.0945 S13: -0.2673 REMARK 3 S21: 0.0367 S22: 0.0032 S23: -0.1372 REMARK 3 S31: 0.3584 S32: -0.0201 S33: 0.1628 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 3ROK 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_1000065185. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAR-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 : 59566 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 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 (%) : 95.9 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.39900 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 (%): 45.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE PH4.0, 0.2M REMARK 280 AMMONIUM ACETATE, 3% ISOPROPANOL, 15% PEG10000, 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 ARG A 45 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 B 247 CB CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 449 O HOH B 363 1455 1.96 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 53.77 -152.55 REMARK 500 ASP A 202 -121.70 63.58 REMARK 500 VAL A 225 -59.86 -121.56 REMARK 500 ARG A 247 -8.91 66.24 REMARK 500 SER B 95 -0.49 74.06 REMARK 500 ARG B 127 -24.94 75.45 REMARK 500 ILE B 128 55.75 -109.25 REMARK 500 ASP B 179 -74.03 -110.91 REMARK 500 ASN B 182 56.66 -92.58 REMARK 500 ASP B 202 -118.74 61.19 REMARK 500 SER B 295 -123.22 -67.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE REAL LEAVING GROUP NICOTINAMIDE OF LIGAND 27C 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: 3ROM 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 3ROK A 45 296 UNP P28907 CD38_HUMAN 45 296 DBREF 3ROK B 45 296 UNP P28907 CD38_HUMAN 45 296 SEQADV 3ROK GLU A 43 UNP P28907 EXPRESSION TAG SEQADV 3ROK PHE A 44 UNP P28907 EXPRESSION TAG SEQADV 3ROK THR A 49 UNP P28907 GLN 49 SEE REMARK 999 SEQADV 3ROK ASP A 100 UNP P28907 ASN 100 ENGINEERED MUTATION SEQADV 3ROK ASP A 164 UNP P28907 ASN 164 ENGINEERED MUTATION SEQADV 3ROK ASP A 209 UNP P28907 ASN 209 ENGINEERED MUTATION SEQADV 3ROK ASP A 219 UNP P28907 ASN 219 ENGINEERED MUTATION SEQADV 3ROK GLU B 43 UNP P28907 EXPRESSION TAG SEQADV 3ROK PHE B 44 UNP P28907 EXPRESSION TAG SEQADV 3ROK THR B 49 UNP P28907 GLN 49 SEE REMARK 999 SEQADV 3ROK ASP B 100 UNP P28907 ASN 100 ENGINEERED MUTATION SEQADV 3ROK ASP B 164 UNP P28907 ASN 164 ENGINEERED MUTATION SEQADV 3ROK ASP B 209 UNP P28907 ASN 209 ENGINEERED MUTATION SEQADV 3ROK 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 27C A 301 17 HET 27C B 301 17 HETNAM 27C 5-O-[(S)-BUTOXY(HYDROXY)PHOSPHORYL]-2-DEOXY-2-FLUORO- HETNAM 2 27C ALPHA-D-ARABINOFURANOSE HETSYN 27C INHIBITOR CZ-27 BASED ON ARABINOSYL-2-FLUORO-2- HETSYN 2 27C DEOXYNICOTINAMIDE MONONUCLEOTIDE, BOUND FORM; 5-O- HETSYN 3 27C [(S)-BUTOXY(HYDROXY)PHOSPHORYL]-2-DEOXY-2-FLUORO- HETSYN 4 27C ALPHA-D-ARABINOSE; 5-O-[(S)-BUTOXY(HYDROXY) HETSYN 5 27C PHOSPHORYL]-2-DEOXY-2-FLUORO-D-ARABINOSE; 5-O-[(S)- HETSYN 6 27C BUTOXY(HYDROXY)PHOSPHORYL]-2-DEOXY-2-FLUORO-ARABINOSE FORMUL 3 27C 2(C9 H18 F O7 P) FORMUL 5 HOH *368(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 ALA A 92 1 12 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 PRO A 118 LYS A 121 5 4 HELIX 7 7 ILE A 128 GLN A 139 1 12 HELIX 8 8 THR A 144 ASP A 147 5 4 HELIX 9 9 THR A 148 ASP A 155 1 8 HELIX 10 10 ASN A 183 ALA A 200 1 18 HELIX 11 11 SER A 220 VAL A 225 1 6 HELIX 12 12 VAL A 225 LEU A 230 1 6 HELIX 13 13 ASP A 252 GLN A 255 5 4 HELIX 14 14 ASP A 256 ARG A 269 1 14 HELIX 15 15 ARG A 280 ASN A 290 1 11 HELIX 16 16 ARG B 58 HIS B 74 1 17 HELIX 17 17 PRO B 75 ARG B 78 5 4 HELIX 18 18 ASP B 81 ILE B 94 1 14 HELIX 19 19 THR B 102 ASP B 105 5 4 HELIX 20 20 TYR B 106 GLY B 113 1 8 HELIX 21 21 ILE B 128 GLN B 139 1 12 HELIX 22 22 THR B 144 ASP B 147 5 4 HELIX 23 23 THR B 148 ASP B 155 1 8 HELIX 24 24 ASN B 183 ALA B 200 1 18 HELIX 25 25 SER B 220 VAL B 225 1 6 HELIX 26 26 GLU B 226 LEU B 230 5 5 HELIX 27 27 ASP B 252 GLN B 255 5 4 HELIX 28 28 ASP B 256 ARG B 269 1 14 HELIX 29 29 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 LYS A 276 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 ILE B 243 N LEU B 208 SHEET 4 E 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 2.09 SSBOND 2 CYS A 99 CYS A 180 1555 1555 2.07 SSBOND 3 CYS A 119 CYS A 201 1555 1555 2.04 SSBOND 4 CYS A 160 CYS A 173 1555 1555 2.06 SSBOND 5 CYS A 254 CYS A 275 1555 1555 2.09 SSBOND 6 CYS A 287 CYS A 296 1555 1555 2.01 SSBOND 7 CYS B 67 CYS B 82 1555 1555 2.09 SSBOND 8 CYS B 99 CYS B 180 1555 1555 2.06 SSBOND 9 CYS B 119 CYS B 201 1555 1555 2.05 SSBOND 10 CYS B 160 CYS B 173 1555 1555 2.12 SSBOND 11 CYS B 254 CYS B 275 1555 1555 2.04 SSBOND 12 CYS B 287 CYS B 296 1555 1555 2.03 LINK OE2 GLU A 226 C1 27C A 301 1555 1555 1.45 LINK OE2 GLU B 226 C1 27C B 301 1555 1555 1.45 CRYST1 41.870 53.658 63.562 109.56 90.95 94.73 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 0.023883 0.001974 0.001130 0.00000 SCALE2 0.000000 0.018700 0.006702 0.00000 SCALE3 0.000000 0.000000 0.016715 0.00000