HEADER HYDROLASE 12-JUL-09 3I9J TITLE CRYSTAL STRUCTURE OF ADP RIBOSYL CYCLASE COMPLEXED WITH A SUBSTRATE TITLE 2 ANALOG AND A PRODUCT NICOTINAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADP-RIBOSYL CYCLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ADRC, NAD(+) NUCLEOSIDASE, NADASE, NAD GLYCOHYDROLASE; COMPND 5 EC: 3.2.2.5; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: APLYSIA CALIFORNICA; SOURCE 3 ORGANISM_COMMON: CALIFORNIA SEA HARE; SOURCE 4 ORGANISM_TAXID: 6500; SOURCE 5 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: X-33 (INVITROGEN); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPICZ(ALPHA)A KEYWDS HOMODIMER, ENZYME-ANALOG-NICOTINAMIDE COMPLEX, ADP-RIBOSYL CYCLASE, KEYWDS 2 DISULFIDE BOND, FERTILIZATION, HYDROLASE, NAD EXPDTA X-RAY DIFFRACTION AUTHOR Q.LIU,R.GRAEFF,I.A.KRIKSUNOV,H.JIANG,B.ZHANG,N.OPPENHEIMER,H.LIN, AUTHOR 2 B.V.L.POTTER,H.C.LEE,Q.HAO REVDAT 6 30-OCT-24 3I9J 1 REMARK REVDAT 5 01-NOV-23 3I9J 1 REMARK REVDAT 4 13-JUL-11 3I9J 1 VERSN REVDAT 3 06-OCT-09 3I9J 1 JRNL REVDAT 2 11-AUG-09 3I9J 1 JRNL REVDAT 1 28-JUL-09 3I9J 0 JRNL AUTH Q.LIU,R.GRAEFF,I.A.KRIKSUNOV,H.JIANG,B.ZHANG,N.OPPENHEIMER, JRNL AUTH 2 H.LIN,B.V.L.POTTER,H.C.LEE,Q.HAO JRNL TITL STRUCTURAL BASIS FOR ENZYMATIC EVOLUTION FROM A DEDICATED JRNL TITL 2 ADP-RIBOSYL CYCLASE TO A MULTIFUNCTIONAL NAD HYDROLASE JRNL REF J.BIOL.CHEM. V. 284 27637 2009 JRNL REFN ISSN 0021-9258 JRNL PMID 19640846 JRNL DOI 10.1074/JBC.M109.031005 REMARK 2 REMARK 2 RESOLUTION. 2.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0067 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) : 2.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 3 NUMBER OF REFLECTIONS : 32751 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1644 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) : 2.18 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.24 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1648 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 68.03 REMARK 3 BIN R VALUE (WORKING SET) : 0.2650 REMARK 3 BIN FREE R VALUE SET COUNT : 76 REMARK 3 BIN FREE R VALUE : 0.3520 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4024 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 90 REMARK 3 SOLVENT ATOMS : 129 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.86000 REMARK 3 B22 (A**2) : 2.86000 REMARK 3 B33 (A**2) : -4.29000 REMARK 3 B12 (A**2) : 1.43000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.246 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.208 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.186 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.709 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.933 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4235 ; 0.022 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5752 ; 1.931 ; 1.986 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 500 ; 6.732 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 196 ;28.975 ;23.571 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 700 ;17.592 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;20.752 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 607 ; 0.128 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3218 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2508 ; 1.018 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4046 ; 1.808 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1727 ; 3.236 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1706 ; 4.948 ; 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 : 2 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 1 A 251 REMARK 3 ORIGIN FOR THE GROUP (A): 2.3990 8.8910 14.4850 REMARK 3 T TENSOR REMARK 3 T11: 0.1562 T22: -0.3261 REMARK 3 T33: -0.1193 T12: 0.1514 REMARK 3 T13: 0.0125 T23: 0.0106 REMARK 3 L TENSOR REMARK 3 L11: 2.0418 L22: 0.7787 REMARK 3 L33: 2.9186 L12: 0.6136 REMARK 3 L13: -0.1882 L23: 0.2215 REMARK 3 S TENSOR REMARK 3 S11: -0.1428 S12: -0.1387 S13: -0.0973 REMARK 3 S21: 0.0866 S22: 0.1179 S23: 0.0177 REMARK 3 S31: -0.4293 S32: -0.3231 S33: 0.0250 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 : B 1 B 251 REMARK 3 ORIGIN FOR THE GROUP (A): 9.1320 -0.5570 -14.5310 REMARK 3 T TENSOR REMARK 3 T11: -0.0713 T22: -0.2701 REMARK 3 T33: -0.0884 T12: -0.1396 REMARK 3 T13: 0.0123 T23: -0.0084 REMARK 3 L TENSOR REMARK 3 L11: 1.4954 L22: 1.5126 REMARK 3 L33: 3.1582 L12: 0.9888 REMARK 3 L13: -0.0468 L23: 0.1242 REMARK 3 S TENSOR REMARK 3 S11: -0.1680 S12: 0.1794 S13: -0.0057 REMARK 3 S21: -0.1268 S22: 0.2024 S23: 0.1048 REMARK 3 S31: -0.0201 S32: -0.1174 S33: -0.0343 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 3I9J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000054134. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUL-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9777 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33025 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.180 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1LBE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M IMIDAZOLE, PH 7.5, 12-24% PEG REMARK 280 4000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 121.56100 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 243.12200 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 182.34150 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 303.90250 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 60.78050 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 LYS A 252 REMARK 465 ARG A 253 REMARK 465 PHE A 254 REMARK 465 TYR A 255 REMARK 465 ARG A 256 REMARK 465 ILE A 257 REMARK 465 ALA A 258 REMARK 465 LYS B 252 REMARK 465 ARG B 253 REMARK 465 PHE B 254 REMARK 465 TYR B 255 REMARK 465 ARG B 256 REMARK 465 ILE B 257 REMARK 465 ALA B 258 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS A 51 CA - CB - SG ANGL. DEV. = 7.5 DEGREES REMARK 500 MET A 105 CG - SD - CE ANGL. DEV. = 10.6 DEGREES 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 TYR A 23 28.68 49.54 REMARK 500 ILE A 26 -44.35 -130.92 REMARK 500 LEU A 53 150.11 -47.66 REMARK 500 ASN A 72 -4.41 84.52 REMARK 500 SER A 108 -0.15 78.29 REMARK 500 LYS A 129 -6.53 -59.93 REMARK 500 GLU A 179 -68.58 -99.13 REMARK 500 CYS A 206 131.01 -37.28 REMARK 500 ALA A 208 136.64 168.81 REMARK 500 ASN A 242 66.50 -167.29 REMARK 500 ALA A 245 145.11 -37.83 REMARK 500 VAL B 80 49.76 -145.62 REMARK 500 SER B 108 -10.58 73.63 REMARK 500 PRO B 126 132.57 -29.70 REMARK 500 ASP B 127 95.35 -52.87 REMARK 500 PHE B 128 -16.62 -49.43 REMARK 500 ALA B 168 -59.09 -29.28 REMARK 500 GLU B 179 -66.27 -100.82 REMARK 500 ASN B 230 59.17 35.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NFD A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AVV B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 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: 3I9K RELATED DB: PDB REMARK 900 ADP-RIBOSYL CYCLASE COMPLEXED WITH NAD REMARK 900 RELATED ID: 3I9L RELATED DB: PDB REMARK 900 ADP-RIBOSYL CYCLASE COMPLEXED WITH N1-CIDPR REMARK 900 RELATED ID: 3I9M RELATED DB: PDB REMARK 900 HUMAN CD38 COMPLEXED WITH ARA-2'F-ADPR REMARK 900 RELATED ID: 3I9N RELATED DB: PDB REMARK 900 HUMAN CD38 COMPLEXED WITH RIBO-2'F-ADPR DBREF 3I9J A 1 258 UNP P29241 NADA_APLCA 25 282 DBREF 3I9J B 1 258 UNP P29241 NADA_APLCA 25 282 SEQRES 1 A 258 ILE VAL PRO THR ARG GLU LEU GLU ASN VAL PHE LEU GLY SEQRES 2 A 258 ARG CYS LYS ASP TYR GLU ILE THR ARG TYR LEU ASP ILE SEQRES 3 A 258 LEU PRO ARG VAL ARG SER ASP CYS SER ALA LEU TRP LYS SEQRES 4 A 258 ASP PHE PHE LYS ALA PHE SER PHE LYS ASN PRO CYS ASP SEQRES 5 A 258 LEU ASP LEU GLY SER TYR LYS ASP PHE PHE THR SER ALA SEQRES 6 A 258 GLN GLN GLN LEU PRO LYS ASN LYS VAL MET PHE TRP SER SEQRES 7 A 258 GLY VAL TYR ASP GLU ALA HIS ASP TYR ALA ASN THR GLY SEQRES 8 A 258 ARG LYS TYR ILE THR LEU GLU ASP THR LEU PRO GLY TYR SEQRES 9 A 258 MET LEU ASN SER LEU VAL TRP CYS GLY GLN ARG ALA ASN SEQRES 10 A 258 PRO GLY PHE ASN GLU LYS VAL CYS PRO ASP PHE LYS THR SEQRES 11 A 258 CYS PRO VAL GLN ALA ARG GLU SER PHE TRP GLY MET ALA SEQRES 12 A 258 SER SER SER TYR ALA HIS SER ALA GLU GLY GLU VAL THR SEQRES 13 A 258 TYR MET VAL ASP GLY SER ASN PRO LYS VAL PRO ALA TYR SEQRES 14 A 258 ARG PRO ASP SER PHE PHE GLY LYS TYR GLU LEU PRO ASN SEQRES 15 A 258 LEU THR ASN LYS VAL THR ARG VAL LYS VAL ILE VAL LEU SEQRES 16 A 258 HIS ARG LEU GLY GLU LYS ILE ILE GLU LYS CYS GLY ALA SEQRES 17 A 258 GLY SER LEU LEU ASP LEU GLU LYS LEU VAL LYS ALA LYS SEQRES 18 A 258 HIS PHE ALA PHE ASP CYS VAL GLU ASN PRO ARG ALA VAL SEQRES 19 A 258 LEU PHE LEU LEU CYS SER ASP ASN PRO ASN ALA ARG GLU SEQRES 20 A 258 CYS ARG LEU ALA LYS ARG PHE TYR ARG ILE ALA SEQRES 1 B 258 ILE VAL PRO THR ARG GLU LEU GLU ASN VAL PHE LEU GLY SEQRES 2 B 258 ARG CYS LYS ASP TYR GLU ILE THR ARG TYR LEU ASP ILE SEQRES 3 B 258 LEU PRO ARG VAL ARG SER ASP CYS SER ALA LEU TRP LYS SEQRES 4 B 258 ASP PHE PHE LYS ALA PHE SER PHE LYS ASN PRO CYS ASP SEQRES 5 B 258 LEU ASP LEU GLY SER TYR LYS ASP PHE PHE THR SER ALA SEQRES 6 B 258 GLN GLN GLN LEU PRO LYS ASN LYS VAL MET PHE TRP SER SEQRES 7 B 258 GLY VAL TYR ASP GLU ALA HIS ASP TYR ALA ASN THR GLY SEQRES 8 B 258 ARG LYS TYR ILE THR LEU GLU ASP THR LEU PRO GLY TYR SEQRES 9 B 258 MET LEU ASN SER LEU VAL TRP CYS GLY GLN ARG ALA ASN SEQRES 10 B 258 PRO GLY PHE ASN GLU LYS VAL CYS PRO ASP PHE LYS THR SEQRES 11 B 258 CYS PRO VAL GLN ALA ARG GLU SER PHE TRP GLY MET ALA SEQRES 12 B 258 SER SER SER TYR ALA HIS SER ALA GLU GLY GLU VAL THR SEQRES 13 B 258 TYR MET VAL ASP GLY SER ASN PRO LYS VAL PRO ALA TYR SEQRES 14 B 258 ARG PRO ASP SER PHE PHE GLY LYS TYR GLU LEU PRO ASN SEQRES 15 B 258 LEU THR ASN LYS VAL THR ARG VAL LYS VAL ILE VAL LEU SEQRES 16 B 258 HIS ARG LEU GLY GLU LYS ILE ILE GLU LYS CYS GLY ALA SEQRES 17 B 258 GLY SER LEU LEU ASP LEU GLU LYS LEU VAL LYS ALA LYS SEQRES 18 B 258 HIS PHE ALA PHE ASP CYS VAL GLU ASN PRO ARG ALA VAL SEQRES 19 B 258 LEU PHE LEU LEU CYS SER ASP ASN PRO ASN ALA ARG GLU SEQRES 20 B 258 CYS ARG LEU ALA LYS ARG PHE TYR ARG ILE ALA HET NFD A 301 45 HET AVV B 301 36 HET NCA B 302 9 HETNAM NFD NICOTINAMIDE 2-FLUORO-ADENINE DINUCLEOTIDE HETNAM AVV [(2R,3S,4R,5R)-5-(6-AMINO-2-FLUORO-9H-PURIN-9-YL)-3,4- HETNAM 2 AVV DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4S)-3,4- HETNAM 3 AVV DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN HETNAM 4 AVV DIPHOSPHATE HETNAM NCA NICOTINAMIDE HETSYN NFD 2-FLUORO-NAD+ HETSYN AVV 2-FLUORO-ADENOSINE DIPHOSPHATE RIBOSE, 2F-ADPRI FORMUL 3 NFD C21 H26 F N7 O14 P2 FORMUL 4 AVV C15 H22 F N5 O13 P2 FORMUL 5 NCA C6 H6 N2 O FORMUL 6 HOH *129(H2 O) HELIX 1 1 GLU A 6 ARG A 22 1 17 HELIX 2 2 ASP A 33 SER A 46 1 14 HELIX 3 3 TYR A 58 GLN A 66 1 9 HELIX 4 4 VAL A 80 ASN A 89 1 10 HELIX 5 5 THR A 96 ASP A 99 5 4 HELIX 6 6 THR A 100 ASN A 107 1 8 HELIX 7 7 ASP A 127 CYS A 131 5 5 HELIX 8 8 PRO A 132 GLU A 137 1 6 HELIX 9 9 GLU A 137 ALA A 151 1 15 HELIX 10 10 SER A 173 GLU A 179 1 7 HELIX 11 11 LEU A 180 LEU A 183 5 4 HELIX 12 12 GLY A 209 LYS A 221 1 13 HELIX 13 13 PRO A 231 ASP A 241 1 11 HELIX 14 14 ALA A 245 ARG A 249 5 5 HELIX 15 15 GLU B 6 ARG B 22 1 17 HELIX 16 16 ASP B 33 SER B 46 1 14 HELIX 17 17 TYR B 58 GLN B 66 1 9 HELIX 18 18 VAL B 80 ASN B 89 1 10 HELIX 19 19 THR B 96 ASP B 99 5 4 HELIX 20 20 THR B 100 ASN B 107 1 8 HELIX 21 21 ASP B 127 CYS B 131 5 5 HELIX 22 22 PRO B 132 GLU B 137 1 6 HELIX 23 23 GLU B 137 ALA B 151 1 15 HELIX 24 24 SER B 173 GLU B 179 1 7 HELIX 25 25 LEU B 180 LEU B 183 5 4 HELIX 26 26 GLY B 209 LYS B 221 1 13 HELIX 27 27 PRO B 231 ASN B 242 1 12 HELIX 28 28 ALA B 245 ARG B 249 5 5 SHEET 1 A 4 VAL A 74 SER A 78 0 SHEET 2 A 4 GLY A 153 ASP A 160 1 O THR A 156 N PHE A 76 SHEET 3 A 4 VAL A 187 LEU A 195 1 O LEU A 195 N VAL A 159 SHEET 4 A 4 ALA A 224 GLU A 229 1 O ALA A 224 N THR A 188 SHEET 1 B 4 MET B 75 SER B 78 0 SHEET 2 B 4 GLY B 153 ASP B 160 1 O THR B 156 N PHE B 76 SHEET 3 B 4 VAL B 187 LEU B 195 1 O LEU B 195 N VAL B 159 SHEET 4 B 4 ALA B 224 GLU B 229 1 O VAL B 228 N VAL B 194 SSBOND 1 CYS A 15 CYS A 34 1555 1555 2.17 SSBOND 2 CYS A 51 CYS A 131 1555 1555 2.06 SSBOND 3 CYS A 112 CYS A 125 1555 1555 2.16 SSBOND 4 CYS A 206 CYS A 227 1555 1555 2.14 SSBOND 5 CYS A 239 CYS A 248 1555 1555 2.09 SSBOND 6 CYS B 15 CYS B 34 1555 1555 2.14 SSBOND 7 CYS B 51 CYS B 131 1555 1555 2.04 SSBOND 8 CYS B 112 CYS B 125 1555 1555 2.11 SSBOND 9 CYS B 206 CYS B 227 1555 1555 2.08 SSBOND 10 CYS B 239 CYS B 248 1555 1555 2.03 CISPEP 1 ASN A 117 PRO A 118 0 2.45 CISPEP 2 ASN B 117 PRO B 118 0 1.04 SITE 1 AC1 13 PHE A 76 TRP A 77 SER A 78 GLY A 79 SITE 2 AC1 13 LEU A 97 GLU A 98 TRP A 140 SER A 144 SITE 3 AC1 13 SER A 173 PHE A 174 PHE A 175 GLU A 179 SITE 4 AC1 13 HOH A 279 SITE 1 AC2 14 PHE B 76 TRP B 77 SER B 78 GLY B 79 SITE 2 AC2 14 ARG B 136 TRP B 140 SER B 144 ARG B 170 SITE 3 AC2 14 SER B 173 PHE B 174 PHE B 175 GLU B 179 SITE 4 AC2 14 HOH B 273 NCA B 302 SITE 1 AC3 5 GLU B 98 ASN B 107 TRP B 140 PHE B 174 SITE 2 AC3 5 AVV B 301 CRYST1 57.121 57.121 364.683 90.00 90.00 120.00 P 61 12 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 0.017507 0.010107 0.000000 0.00000 SCALE2 0.000000 0.020215 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002742 0.00000