HEADER HYDROLASE 02-AUG-11 3ZWN TITLE CRYSTAL STRUCTURE OF APLYSIA CYCLASE COMPLEXED WITH SUBSTRATE NGD AND TITLE 2 PRODUCT CGDPR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADP-RIBOSYL CYCLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ADRC, NAD GLYCOHYDROLASE, NAD(+) NUCLEOSIDASE, NADASE; 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; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PPICZALPHAA KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.KOTAKA,R.GRAEFF,L.H.ZHANG,H.C.LEE,Q.HAO REVDAT 3 20-DEC-23 3ZWN 1 COMPND REMARK HETNAM REVDAT 2 25-JAN-12 3ZWN 1 AUTHOR JRNL REVDAT 1 30-NOV-11 3ZWN 0 JRNL AUTH M.KOTAKA,R.GRAEFF,Z.CHEN,L.H.ZHANG,H.C.LEE,Q.HAO JRNL TITL STRUCTURAL STUDIES OF INTERMEDIATES ALONG THE CYCLIZATION JRNL TITL 2 PATHWAY OF APLYSIA ADP-RIBOSYL CYCLASE. JRNL REF J.MOL.BIOL. V. 415 514 2012 JRNL REFN ISSN 0022-2836 JRNL PMID 22138343 JRNL DOI 10.1016/J.JMB.2011.11.022 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 46173 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2484 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2442 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 68.27 REMARK 3 BIN R VALUE (WORKING SET) : 0.2620 REMARK 3 BIN FREE R VALUE SET COUNT : 133 REMARK 3 BIN FREE R VALUE : 0.3010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4039 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 81 REMARK 3 SOLVENT ATOMS : 452 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.13000 REMARK 3 B22 (A**2) : -0.38000 REMARK 3 B33 (A**2) : 0.09000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.10000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.133 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.137 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.084 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.003 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4242 ; 0.024 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5766 ; 2.071 ; 1.986 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 503 ; 5.984 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 196 ;29.653 ;23.571 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 700 ;14.963 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;20.227 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 615 ; 0.178 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3221 ; 0.011 ; 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): 2523 ; 1.200 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4067 ; 2.049 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1719 ; 3.331 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1699 ; 5.222 ; 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 : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A -1 A 251 REMARK 3 RESIDUE RANGE : A 2458 A 2458 REMARK 3 ORIGIN FOR THE GROUP (A): 39.2975 1.5158 19.7319 REMARK 3 T TENSOR REMARK 3 T11: 0.0522 T22: 0.0399 REMARK 3 T33: 0.0159 T12: -0.0059 REMARK 3 T13: 0.0070 T23: 0.0125 REMARK 3 L TENSOR REMARK 3 L11: 0.6496 L22: 0.7145 REMARK 3 L33: 0.3622 L12: -0.2012 REMARK 3 L13: -0.1629 L23: 0.2992 REMARK 3 S TENSOR REMARK 3 S11: -0.0022 S12: -0.0221 S13: -0.0230 REMARK 3 S21: 0.0243 S22: -0.0053 S23: -0.0574 REMARK 3 S31: -0.0254 S32: 0.0248 S33: 0.0074 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 0 B 251 REMARK 3 RESIDUE RANGE : B 5573 B 5573 REMARK 3 ORIGIN FOR THE GROUP (A): 9.6721 -1.5186 10.9168 REMARK 3 T TENSOR REMARK 3 T11: 0.0271 T22: 0.0053 REMARK 3 T33: 0.0151 T12: 0.0009 REMARK 3 T13: 0.0055 T23: 0.0037 REMARK 3 L TENSOR REMARK 3 L11: 0.5938 L22: 0.4714 REMARK 3 L33: 0.5011 L12: 0.1812 REMARK 3 L13: 0.2534 L23: 0.4099 REMARK 3 S TENSOR REMARK 3 S11: -0.0169 S12: -0.0196 S13: -0.0468 REMARK 3 S21: -0.0429 S22: 0.0005 S23: 0.0307 REMARK 3 S31: -0.0315 S32: -0.0113 S33: 0.0164 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 3ZWN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1290049232. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAY-09 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 : NSRRC REMARK 200 BEAMLINE : BL13B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48804 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.400 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 69.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.55000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 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 1R12 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M IMIDAZOLE, PH 7.5, 12-14% PEG REMARK 280 4000. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 28.92600 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: 4500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.2 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 ALA B -1 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: 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 OD2 ASP A 33 O HOH A 3083 1.73 REMARK 500 O HOH B 6052 O HOH B 6122 1.78 REMARK 500 OD1 ASP A 172 O HOH A 3194 1.88 REMARK 500 O HOH A 3086 O HOH A 3158 2.00 REMARK 500 O ALA B 251 O HOH B 6208 2.02 REMARK 500 NH1 ARG B 246 O HOH B 6207 2.03 REMARK 500 O HOH A 3015 O HOH B 6032 2.06 REMARK 500 O HOH B 6030 O HOH B 6052 2.11 REMARK 500 REMARK 500 REMARK: NULL 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 CB ASP B 25 O HOH A 3239 2655 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ASP A 33 CB ASP A 33 CG -0.143 REMARK 500 PHE B 174 CB PHE B 174 CG -0.114 REMARK 500 REMARK 500 REMARK: NULL 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 ARG B 29 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ASP B 33 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 LEU B 106 CA - CB - CG ANGL. DEV. = -17.6 DEGREES REMARK 500 LEU B 106 CB - CG - CD1 ANGL. DEV. = 11.0 DEGREES REMARK 500 LEU B 106 CB - CG - CD2 ANGL. DEV. = 12.4 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 SER A 108 -4.85 76.09 REMARK 500 ASN A 230 62.12 37.89 REMARK 500 ASN A 242 67.45 -151.54 REMARK 500 ASN B 89 60.21 66.28 REMARK 500 THR B 90 57.80 36.55 REMARK 500 SER B 108 -3.45 69.52 REMARK 500 PHE B 128 75.91 -69.31 REMARK 500 LYS B 129 -20.53 169.85 REMARK 500 GLU B 179 -61.65 -97.80 REMARK 500 ASN B 242 69.18 -153.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A3035 DISTANCE = 5.83 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CGR A 2458 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NGD B 5573 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1R0S RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ADP-RIBOSYL CYCLASE GLU179ALA MUTANT REMARK 900 RELATED ID: 1LBE RELATED DB: PDB REMARK 900 APLYSIA ADP RIBOSYL CYCLASE REMARK 900 RELATED ID: 1R16 RELATED DB: PDB REMARK 900 APLYSIA ADP RIBOSYL CYCLASE WITH BOUND PYRIDYLCARBINOL ANDR5P REMARK 900 RELATED ID: 1R12 RELATED DB: PDB REMARK 900 NATIVE APLYSIA ADP RIBOSYL CYCLASE REMARK 900 RELATED ID: 1R15 RELATED DB: PDB REMARK 900 APLYSIA ADP RIBOSYL CYCLASE WITH BOUND NICOTINAMIDE AND R5P REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE ADDITIONAL ALANINE AT THE N-TERMINUS ARE ACTUALLY AMINO ACIDS REMARK 999 LEFT OVER FROM THE CLEAVAGE OF THE SECRETORY SIGNALLING PROTEIN REMARK 999 FOR SECRETION DURING EXPRESSION FROM PICHIA. DBREF 3ZWN A 1 258 UNP P29241 NADA_APLCA 25 282 DBREF 3ZWN B 1 258 UNP P29241 NADA_APLCA 25 282 SEQADV 3ZWN ALA A -1 UNP P29241 EXPRESSION TAG SEQADV 3ZWN ALA A 0 UNP P29241 EXPRESSION TAG SEQADV 3ZWN ALA B -1 UNP P29241 EXPRESSION TAG SEQADV 3ZWN ALA B 0 UNP P29241 EXPRESSION TAG SEQRES 1 A 260 ALA ALA ILE VAL PRO THR ARG GLU LEU GLU ASN VAL PHE SEQRES 2 A 260 LEU GLY ARG CYS LYS ASP TYR GLU ILE THR ARG TYR LEU SEQRES 3 A 260 ASP ILE LEU PRO ARG VAL ARG SER ASP CYS SER ALA LEU SEQRES 4 A 260 TRP LYS ASP PHE PHE LYS ALA PHE SER PHE LYS ASN PRO SEQRES 5 A 260 CYS ASP LEU ASP LEU GLY SER TYR LYS ASP PHE PHE THR SEQRES 6 A 260 SER ALA GLN GLN GLN LEU PRO LYS ASN LYS VAL MET PHE SEQRES 7 A 260 TRP SER GLY VAL TYR ASP GLU ALA HIS ASP TYR ALA ASN SEQRES 8 A 260 THR GLY ARG LYS TYR ILE THR LEU GLU ASP THR LEU PRO SEQRES 9 A 260 GLY TYR MET LEU ASN SER LEU VAL TRP CYS GLY GLN ARG SEQRES 10 A 260 ALA ASN PRO GLY PHE ASN GLU LYS VAL CYS PRO ASP PHE SEQRES 11 A 260 LYS THR CYS PRO VAL GLN ALA ARG GLU SER PHE TRP GLY SEQRES 12 A 260 MET ALA SER SER SER TYR ALA HIS SER ALA GLU GLY GLU SEQRES 13 A 260 VAL THR TYR MET VAL ASP GLY SER ASN PRO LYS VAL PRO SEQRES 14 A 260 ALA TYR ARG PRO ASP SER PHE PHE GLY LYS TYR GLU LEU SEQRES 15 A 260 PRO ASN LEU THR ASN LYS VAL THR ARG VAL LYS VAL ILE SEQRES 16 A 260 VAL LEU HIS ARG LEU GLY GLU LYS ILE ILE GLU LYS CYS SEQRES 17 A 260 GLY ALA GLY SER LEU LEU ASP LEU GLU LYS LEU VAL LYS SEQRES 18 A 260 ALA LYS HIS PHE ALA PHE ASP CYS VAL GLU ASN PRO ARG SEQRES 19 A 260 ALA VAL LEU PHE LEU LEU CYS SER ASP ASN PRO ASN ALA SEQRES 20 A 260 ARG GLU CYS ARG LEU ALA LYS ARG PHE TYR ARG ILE ALA SEQRES 1 B 260 ALA ALA ILE VAL PRO THR ARG GLU LEU GLU ASN VAL PHE SEQRES 2 B 260 LEU GLY ARG CYS LYS ASP TYR GLU ILE THR ARG TYR LEU SEQRES 3 B 260 ASP ILE LEU PRO ARG VAL ARG SER ASP CYS SER ALA LEU SEQRES 4 B 260 TRP LYS ASP PHE PHE LYS ALA PHE SER PHE LYS ASN PRO SEQRES 5 B 260 CYS ASP LEU ASP LEU GLY SER TYR LYS ASP PHE PHE THR SEQRES 6 B 260 SER ALA GLN GLN GLN LEU PRO LYS ASN LYS VAL MET PHE SEQRES 7 B 260 TRP SER GLY VAL TYR ASP GLU ALA HIS ASP TYR ALA ASN SEQRES 8 B 260 THR GLY ARG LYS TYR ILE THR LEU GLU ASP THR LEU PRO SEQRES 9 B 260 GLY TYR MET LEU ASN SER LEU VAL TRP CYS GLY GLN ARG SEQRES 10 B 260 ALA ASN PRO GLY PHE ASN GLU LYS VAL CYS PRO ASP PHE SEQRES 11 B 260 LYS THR CYS PRO VAL GLN ALA ARG GLU SER PHE TRP GLY SEQRES 12 B 260 MET ALA SER SER SER TYR ALA HIS SER ALA GLU GLY GLU SEQRES 13 B 260 VAL THR TYR MET VAL ASP GLY SER ASN PRO LYS VAL PRO SEQRES 14 B 260 ALA TYR ARG PRO ASP SER PHE PHE GLY LYS TYR GLU LEU SEQRES 15 B 260 PRO ASN LEU THR ASN LYS VAL THR ARG VAL LYS VAL ILE SEQRES 16 B 260 VAL LEU HIS ARG LEU GLY GLU LYS ILE ILE GLU LYS CYS SEQRES 17 B 260 GLY ALA GLY SER LEU LEU ASP LEU GLU LYS LEU VAL LYS SEQRES 18 B 260 ALA LYS HIS PHE ALA PHE ASP CYS VAL GLU ASN PRO ARG SEQRES 19 B 260 ALA VAL LEU PHE LEU LEU CYS SER ASP ASN PRO ASN ALA SEQRES 20 B 260 ARG GLU CYS ARG LEU ALA LYS ARG PHE TYR ARG ILE ALA HET CGR A2458 36 HET NGD B5573 45 HETNAM CGR CYCLIC GUANOSINE DIPHOSPHATE-RIBOSE HETNAM NGD 3-(AMINOCARBONYL)-1-[(2R,3R,4S,5R)-5-({[(S)-{[(S)- HETNAM 2 NGD {[(2R,3S,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN- HETNAM 3 NGD 9-YL)-3,4-DIHYD ROXYTETRAHYDROFURAN-2- HETNAM 4 NGD YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY) HETNAM 5 NGD PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2- HETNAM 6 NGD YL]PYRIDINIUM HETSYN CGR CYCLIC GDP-RIBOSE HETSYN NGD NICOTINAMIDE GUANINE DINUCLEOTIDE FORMUL 3 CGR C15 H23 N5 O14 P2 FORMUL 4 NGD C21 H28 N7 O15 P2 1+ FORMUL 5 HOH *452(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 ASN A 49 LEU A 53 5 5 HELIX 4 4 TYR A 58 GLN A 66 1 9 HELIX 5 5 VAL A 80 ASN A 89 1 10 HELIX 6 6 THR A 96 ASP A 99 5 4 HELIX 7 7 THR A 100 ASN A 107 1 8 HELIX 8 8 PHE A 128 CYS A 131 5 4 HELIX 9 9 PRO A 132 GLU A 137 1 6 HELIX 10 10 GLU A 137 ALA A 151 1 15 HELIX 11 11 SER A 173 GLU A 179 1 7 HELIX 12 12 LEU A 180 LEU A 183 5 4 HELIX 13 13 ALA A 208 LYS A 221 1 14 HELIX 14 14 PRO A 231 ASN A 242 1 12 HELIX 15 15 ALA A 245 ARG A 249 5 5 HELIX 16 16 GLU B 6 ARG B 22 1 17 HELIX 17 17 ASP B 33 SER B 46 1 14 HELIX 18 18 TYR B 58 GLN B 66 1 9 HELIX 19 19 VAL B 80 ASN B 89 1 10 HELIX 20 20 THR B 96 ASP B 99 5 4 HELIX 21 21 THR B 100 ASN B 107 1 8 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 ALA B 208 LYS B 221 1 14 HELIX 27 27 PRO B 231 ASN B 242 1 12 HELIX 28 28 ALA B 245 ARG B 249 5 5 SHEET 1 AA 2 ALA A 0 ILE A 1 0 SHEET 2 AA 2 CYS A 125 PRO A 126 -1 O CYS A 125 N ILE A 1 SHEET 1 AB 4 VAL A 74 SER A 78 0 SHEET 2 AB 4 GLY A 153 ASP A 160 1 O GLU A 154 N VAL A 74 SHEET 3 AB 4 VAL A 187 LEU A 195 1 N THR A 188 O GLY A 153 SHEET 4 AB 4 ALA A 224 GLU A 229 1 O ALA A 224 N VAL A 190 SHEET 1 BA 4 VAL B 74 SER B 78 0 SHEET 2 BA 4 GLY B 153 ASP B 160 1 O GLU B 154 N VAL B 74 SHEET 3 BA 4 VAL B 187 LEU B 195 1 N THR B 188 O GLY B 153 SHEET 4 BA 4 ALA B 224 GLU B 229 1 O ALA B 224 N VAL B 190 SSBOND 1 CYS A 15 CYS A 34 1555 1555 2.07 SSBOND 2 CYS A 51 CYS A 131 1555 1555 2.04 SSBOND 3 CYS A 112 CYS A 125 1555 1555 2.05 SSBOND 4 CYS A 206 CYS A 227 1555 1555 2.08 SSBOND 5 CYS A 239 CYS A 248 1555 1555 2.06 SSBOND 6 CYS B 15 CYS B 34 1555 1555 2.12 SSBOND 7 CYS B 51 CYS B 131 1555 1555 2.02 SSBOND 8 CYS B 112 CYS B 125 1555 1555 2.08 SSBOND 9 CYS B 206 CYS B 227 1555 1555 2.08 SSBOND 10 CYS B 239 CYS B 248 1555 1555 2.04 CISPEP 1 ASN A 117 PRO A 118 0 0.08 CISPEP 2 ASN B 117 PRO B 118 0 4.76 SITE 1 AC1 19 PHE A 76 TRP A 77 SER A 78 GLY A 79 SITE 2 AC1 19 LEU A 97 GLU A 98 ASN A 107 TRP A 140 SITE 3 AC1 19 SER A 144 ARG A 170 SER A 173 PHE A 174 SITE 4 AC1 19 PHE A 175 GLU A 179 HOH A3135 HOH A3156 SITE 5 AC1 19 HOH A3172 HOH A3193 HOH A3241 SITE 1 AC2 24 PHE B 76 TRP B 77 SER B 78 GLY B 79 SITE 2 AC2 24 LEU B 97 GLU B 98 ASN B 107 PHE B 128 SITE 3 AC2 24 ARG B 136 TRP B 140 SER B 144 ARG B 170 SITE 4 AC2 24 SER B 173 PHE B 174 PHE B 175 GLU B 179 SITE 5 AC2 24 HOH B6101 HOH B6120 HOH B6140 HOH B6162 SITE 6 AC2 24 HOH B6163 HOH B6209 HOH B6210 HOH B6211 CRYST1 69.494 57.852 71.303 90.00 100.94 90.00 P 1 21 1 4 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 0.014390 0.000000 0.002781 0.00000 SCALE2 0.000000 0.017285 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014284 0.00000 MTRIX1 1 -0.863900 -0.360300 -0.352000 51.15120 1 MTRIX2 1 -0.390300 0.037200 0.919900 -4.72200 1 MTRIX3 1 -0.318400 0.932100 -0.172700 25.95240 1