HEADER HYDROLASE 12-JUL-09 3I9O TITLE CRYSTAL STRUCTURE OF ADP RIBOSYL CYCLASE COMPLEXED WITH RIBO-2'F-ADP TITLE 2 RIBOSE 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-REACTION-INTERMEDIATE COMPLEX, ADP-RIBOSYL CYCLASE, KEYWDS 2 DISULFIDE BOND, FERTILIZATION, HYDROLASE, NAD EXPDTA X-RAY DIFFRACTION AUTHOR R.GRAEFF,Q.LIU,I.A.KRIKSUNOV,M.KOTAKA,N.OPPENHEIMER,Q.HAO,H.C.LEE REVDAT 6 25-DEC-24 3I9O 1 REMARK LINK REVDAT 5 01-NOV-23 3I9O 1 REMARK HETSYN LINK REVDAT 4 13-JUL-11 3I9O 1 VERSN REVDAT 3 06-OCT-09 3I9O 1 JRNL REVDAT 2 11-AUG-09 3I9O 1 JRNL REVDAT 1 28-JUL-09 3I9O 0 JRNL AUTH R.GRAEFF,Q.LIU,I.A.KRIKSUNOV,M.KOTAKA,N.OPPENHEIMER,Q.HAO, JRNL AUTH 2 H.C.LEE JRNL TITL MECHANISM OF CYCLIZING NAD TO CYCLIC ADP-RIBOSE BY JRNL TITL 2 ADP-RIBOSYL CYCLASE AND CD38 JRNL REF J.BIOL.CHEM. V. 284 27629 2009 JRNL REFN ISSN 0021-9258 JRNL PMID 19640843 JRNL DOI 10.1074/JBC.M109.030965 REMARK 2 REMARK 2 RESOLUTION. 3.00 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 12358 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) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 627 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) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 872 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.29 REMARK 3 BIN R VALUE (WORKING SET) : 0.3080 REMARK 3 BIN FREE R VALUE SET COUNT : 49 REMARK 3 BIN FREE R VALUE : 0.4120 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 : 70 REMARK 3 SOLVENT ATOMS : 0 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) : 45.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.94000 REMARK 3 B22 (A**2) : 2.94000 REMARK 3 B33 (A**2) : -4.41000 REMARK 3 B12 (A**2) : 1.47000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.492 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.353 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 44.047 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.914 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.877 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4214 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5722 ; 1.980 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 500 ; 6.428 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 196 ;34.284 ;23.571 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 700 ;21.258 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;19.744 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 606 ; 0.109 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3194 ; 0.008 ; 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 ; 0.321 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4046 ; 0.676 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1706 ; 1.339 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1676 ; 2.208 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1 A 251 3 REMARK 3 1 B 1 B 251 3 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 1004 ; 0.090 ; 0.050 REMARK 3 LOOSE POSITIONAL 1 B (A): 1008 ; 0.130 ; 5.000 REMARK 3 TIGHT THERMAL 1 A (A**2): 1004 ; 0.080 ; 0.500 REMARK 3 LOOSE THERMAL 1 B (A**2): 1008 ; 0.100 ;10.000 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): -2.7023 -9.2783 14.4030 REMARK 3 T TENSOR REMARK 3 T11: -0.0036 T22: -0.2411 REMARK 3 T33: -0.1644 T12: 0.1329 REMARK 3 T13: 0.0208 T23: -0.0063 REMARK 3 L TENSOR REMARK 3 L11: 2.5179 L22: 1.2115 REMARK 3 L33: 3.6104 L12: 0.2625 REMARK 3 L13: -0.1825 L23: -0.4022 REMARK 3 S TENSOR REMARK 3 S11: -0.1274 S12: -0.2263 S13: 0.0898 REMARK 3 S21: 0.0442 S22: 0.0945 S23: -0.0477 REMARK 3 S31: 0.3189 S32: 0.4628 S33: 0.0329 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): -9.5341 0.4536 -14.2355 REMARK 3 T TENSOR REMARK 3 T11: -0.0436 T22: -0.2740 REMARK 3 T33: -0.1726 T12: -0.0683 REMARK 3 T13: 0.0113 T23: -0.0120 REMARK 3 L TENSOR REMARK 3 L11: 2.4074 L22: 2.2529 REMARK 3 L33: 3.0447 L12: 1.2775 REMARK 3 L13: 0.0687 L23: -0.2983 REMARK 3 S TENSOR REMARK 3 S11: -0.0991 S12: 0.2424 S13: -0.0448 REMARK 3 S21: -0.1867 S22: 0.2319 S23: -0.1391 REMARK 3 S31: 0.0215 S32: 0.2040 S33: -0.1328 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; BOTH LINKS ARE COVALENT INTERMEDIATES RESULTS FROM REMARK 3 BIOCHEMICAL REACTION. REMARK 4 REMARK 4 3I9O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000054139. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-08 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) : 0.9789 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 : 12475 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 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 (%) : 95.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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 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 (%): 56.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M 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 120.11100 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 240.22200 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 180.16650 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 300.27750 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 60.05550 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: 2860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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: 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 OE2 GLU B 179 C1'N AVW B 301 1.84 REMARK 500 OE2 GLU A 179 C1'N AVW A 301 2.19 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 CYS A 51 CB CYS A 51 SG 0.112 REMARK 500 VAL A 228 CB VAL A 228 CG2 -0.161 REMARK 500 ASN B 49 CB ASN B 49 CG -0.152 REMARK 500 ASP B 127 CB ASP B 127 CG -0.164 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 VAL A 228 CG1 - CB - CG2 ANGL. DEV. = -15.3 DEGREES REMARK 500 ARG A 246 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG A 249 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ASP B 127 CB - CA - C ANGL. DEV. = -15.7 DEGREES REMARK 500 ASP B 127 CB - CG - OD1 ANGL. DEV. = -12.2 DEGREES REMARK 500 LEU B 195 CB - CG - CD2 ANGL. DEV. = -14.6 DEGREES REMARK 500 ARG B 249 CG - CD - NE ANGL. DEV. = 17.7 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 ASP A 54 -164.49 -122.70 REMARK 500 VAL A 80 41.01 -146.09 REMARK 500 ASN A 89 73.22 55.77 REMARK 500 THR A 90 53.68 29.41 REMARK 500 SER A 108 -2.22 81.28 REMARK 500 LYS A 123 -64.88 -92.95 REMARK 500 LYS A 129 4.80 -54.74 REMARK 500 ARG A 136 -37.55 -38.07 REMARK 500 GLU A 179 -74.30 -84.32 REMARK 500 PRO A 181 -6.44 -55.98 REMARK 500 ASN A 242 58.51 -170.27 REMARK 500 ARG A 246 -37.17 -34.07 REMARK 500 GLU B 19 -39.56 -39.69 REMARK 500 ASN B 49 155.85 -49.78 REMARK 500 ASP B 54 -169.36 -124.67 REMARK 500 LYS B 71 129.74 -39.79 REMARK 500 ASN B 72 10.77 59.81 REMARK 500 SER B 108 -1.71 84.64 REMARK 500 ASN B 117 139.73 -38.84 REMARK 500 PHE B 128 -36.71 84.67 REMARK 500 ARG B 136 -42.48 -27.15 REMARK 500 ALA B 224 -175.16 -65.25 REMARK 500 PHE B 225 129.30 -170.89 REMARK 500 ASN B 242 61.80 -154.54 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 AVW A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AVW B 301 DBREF 3I9O A 1 258 UNP P29241 NADA_APLCA 25 282 DBREF 3I9O 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 AVW A 301 35 HET AVW B 301 35 HETNAM AVW [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4- HETNAM 2 AVW DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL [(2R,3R,4S)-4- HETNAM 3 AVW FLUORO-3-HYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN HETNAM 4 AVW DIPHOSPHATE HETSYN AVW RIBOSYL-2-FLUORO-DEOXY-ADENOSINE DIPHOSPHATE RIBOSE; HETSYN 2 AVW RIBO-2'F-ADPR FORMUL 3 AVW 2(C15 H22 F N5 O12 P2) 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 TYR A 178 1 6 HELIX 11 11 GLU A 179 LEU A 183 5 5 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 ALA B 65 1 8 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 PRO B 132 GLU B 137 1 6 HELIX 22 22 GLU B 137 SER B 150 1 14 HELIX 23 23 SER B 173 GLU B 179 1 7 HELIX 24 24 LEU B 180 LEU B 183 5 4 HELIX 25 25 GLY B 209 LYS B 221 1 13 HELIX 26 26 PRO B 231 ASP B 241 1 11 HELIX 27 27 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 ILE A 193 N TYR A 157 SHEET 4 A 4 ALA A 224 GLU A 229 1 O VAL A 228 N VAL A 194 SHEET 1 B 4 VAL B 74 TRP B 77 0 SHEET 2 B 4 GLY B 153 ASP B 160 1 O THR B 156 N VAL B 74 SHEET 3 B 4 VAL B 187 LEU B 195 1 O ILE B 193 N TYR B 157 SHEET 4 B 4 ASP B 226 GLU B 229 1 O VAL B 228 N VAL B 194 SSBOND 1 CYS A 15 CYS A 34 1555 1555 2.15 SSBOND 2 CYS A 51 CYS A 131 1555 1555 2.08 SSBOND 3 CYS A 112 CYS A 125 1555 1555 2.11 SSBOND 4 CYS A 206 CYS A 227 1555 1555 2.11 SSBOND 5 CYS A 239 CYS A 248 1555 1555 2.03 SSBOND 6 CYS B 15 CYS B 34 1555 1555 2.12 SSBOND 7 CYS B 51 CYS B 131 1555 1555 2.10 SSBOND 8 CYS B 112 CYS B 125 1555 1555 2.07 SSBOND 9 CYS B 206 CYS B 227 1555 1555 2.12 SSBOND 10 CYS B 239 CYS B 248 1555 1555 2.05 CISPEP 1 ASN A 117 PRO A 118 0 4.25 CISPEP 2 ASN B 117 PRO B 118 0 6.61 SITE 1 AC1 10 PHE A 76 TRP A 77 SER A 78 GLY A 79 SITE 2 AC1 10 TYR A 81 SER A 144 SER A 173 PHE A 174 SITE 3 AC1 10 PHE A 175 GLU A 179 SITE 1 AC2 11 PHE B 76 TRP B 77 SER B 78 GLY B 79 SITE 2 AC2 11 LEU B 97 TRP B 140 SER B 144 SER B 173 SITE 3 AC2 11 PHE B 174 PHE B 175 GLU B 179 CRYST1 56.726 56.726 360.333 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 0.017629 0.010178 0.000000 0.00000 SCALE2 0.000000 0.020356 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002775 0.00000