HEADER TRANSFERASE 21-MAY-08 2VU5 TITLE CRYSTAL STRUCTURE OF PNDK FROM BACILLUS ANTHRACIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DIPHOSPHATE KINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NDK, NDP KINASE, NUCLEOSIDE-2-P KINASE; COMPND 5 EC: 2.7.4.6; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS ANTHRACIS; SOURCE 3 ORGANISM_TAXID: 1392; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS BACILLUS ANTHRACIS, NUCLEOTIDE-BINDING, ATP-BINDING, METAL-BINDING, KEYWDS 2 PHOSPHOPROTEIN, NUCLEOTIDE METABOLISM, NUCLEOSIDE DIPHOSPHATE KEYWDS 3 KINASE, KINASE, CYTOPLASM, MAGNESIUM, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.MISRA,A.AGGARWAL,D.DUBE,M.S.ZAMAN,Y.SINGH,R.RAMACHANDRAN REVDAT 3 08-MAY-24 2VU5 1 REMARK REVDAT 2 14-JUL-09 2VU5 1 VERSN JRNL REVDAT 1 10-MAR-09 2VU5 0 JRNL AUTH G.MISRA,A.AGGARWAL,D.DUBE,M.S.ZAMAN,Y.SINGH,R.RAMACHANDRAN JRNL TITL CRYSTAL STRUCTURE OF THE BACILLUS ANTHRACIS NUCLEOSIDE JRNL TITL 2 DIPHOSPHATE KINASE AND ITS CHARACTERIZATION REVEALS AN JRNL TITL 3 ENZYME ADAPTED TO PERFORM UNDER STRESS CONDITIONS. JRNL REF PROTEINS V. 76 496 2009 JRNL REFN ISSN 0887-3585 JRNL PMID 19241473 JRNL DOI 10.1002/PROT.22364 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 93.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 11540 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.500 REMARK 3 FREE R VALUE TEST SET COUNT : 931 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 833 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2330 REMARK 3 BIN FREE R VALUE SET COUNT : 63 REMARK 3 BIN FREE R VALUE : 0.2960 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1170 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 80 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.08000 REMARK 3 B22 (A**2) : -0.08000 REMARK 3 B33 (A**2) : 0.12000 REMARK 3 B12 (A**2) : -0.04000 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): 0.152 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.148 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.097 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.441 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1156 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1559 ; 1.500 ; 1.945 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 146 ; 5.840 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 51 ;40.172 ;23.922 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 189 ;16.169 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;29.035 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 168 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 881 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 443 ; 0.230 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 793 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 63 ; 0.123 ; 0.200 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): 46 ; 0.173 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.333 ; 0.200 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): 746 ; 1.135 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1156 ; 1.860 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 463 ; 3.091 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 403 ; 5.390 ; 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 : NULL 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 2VU5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1290036338. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : YALE MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12490 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 26.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/2 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 0.00000 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 0.00000 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 26.15050 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 26.15050 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 26.15050 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 26.15050 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 26.15050 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 26.15050 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 17740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 41740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -113.4 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 26.15050 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -53.76550 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 93.12458 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -0.500000 -0.866025 0.000000 53.76550 REMARK 350 BIOMT2 4 0.866025 -0.500000 0.000000 93.12458 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 0.500000 0.866025 0.000000 -53.76550 REMARK 350 BIOMT2 5 0.866025 -0.500000 0.000000 93.12458 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 26.15050 REMARK 350 BIOMT1 6 0.500000 -0.866025 0.000000 53.76550 REMARK 350 BIOMT2 6 -0.866025 -0.500000 0.000000 93.12458 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 26.15050 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2029 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2030 LIES ON A SPECIAL POSITION. REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 VAL A 13 C O CG1 CG2 REMARK 480 LYS A 27 CG CD CE NZ REMARK 480 GLU A 43 CG CD OE1 OE2 REMARK 480 GLN A 47 CG CD OE1 REMARK 480 GLU A 53 CG CD OE1 OE2 REMARK 480 GLU A 54 CG CD OE1 OE2 REMARK 480 LYS A 55 CG CD CE NZ REMARK 480 ASP A 63 CG OD1 OD2 REMARK 480 HIS A 94 CG ND1 CD2 CE1 NE2 REMARK 480 MET A 143 CG SD CE 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 13 CG1 - CB - CG2 ANGL. DEV. = 10.6 DEGREES REMARK 500 GLN A 47 OE1 - CD - NE2 ANGL. DEV. = -33.3 DEGREES REMARK 500 GLU A 53 CA - CB - CG ANGL. DEV. = 14.4 DEGREES REMARK 500 GLU A 54 CA - CB - CG ANGL. DEV. = 14.6 DEGREES REMARK 500 ARG A 102 NE - CZ - NH1 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG A 102 NE - CZ - NH2 ANGL. DEV. = 4.9 DEGREES REMARK 500 MET A 143 CG - SD - CE ANGL. DEV. = 10.0 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 ILE A 113 -48.89 80.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 GLN A 47 0.18 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2VU5 A 1 148 UNP Q81SV8 NDK_BACAN 1 148 SEQADV 2VU5 GLU A 53 UNP Q81SV8 THR 53 CONFLICT SEQRES 1 A 148 MET GLU LYS THR PHE LEU MET VAL LYS PRO ASP GLY VAL SEQRES 2 A 148 GLN ARG ALA PHE ILE GLY GLU ILE VAL ALA ARG PHE GLU SEQRES 3 A 148 LYS LYS GLY PHE GLN LEU VAL GLY ALA LYS LEU MET GLN SEQRES 4 A 148 VAL THR PRO GLU ILE ALA GLY GLN HIS TYR ALA GLU HIS SEQRES 5 A 148 GLU GLU LYS PRO PHE PHE GLY GLU LEU VAL ASP PHE ILE SEQRES 6 A 148 THR SER GLY PRO VAL PHE ALA MET VAL TRP GLN GLY GLU SEQRES 7 A 148 GLY VAL VAL ASP THR ALA ARG ASN MET MET GLY LYS THR SEQRES 8 A 148 ARG PRO HIS GLU ALA ALA PRO GLY THR ILE ARG GLY ASP SEQRES 9 A 148 PHE GLY VAL THR VAL ALA LYS ASN ILE ILE HIS GLY SER SEQRES 10 A 148 ASP SER LEU GLU SER ALA GLU ARG GLU ILE GLY ILE PHE SEQRES 11 A 148 PHE LYS GLU GLU GLU LEU VAL ASP TYR SER LYS LEU MET SEQRES 12 A 148 ASN GLU TRP ILE TYR FORMUL 2 HOH *80(H2 O) HELIX 1 1 LYS A 9 ARG A 15 1 7 HELIX 2 2 PHE A 17 GLY A 29 1 13 HELIX 3 3 THR A 41 HIS A 48 1 8 HELIX 4 4 TYR A 49 HIS A 52 5 4 HELIX 5 5 PRO A 56 ILE A 65 1 10 HELIX 6 6 GLY A 79 GLY A 89 1 11 HELIX 7 7 THR A 100 GLY A 106 1 7 HELIX 8 8 SER A 119 PHE A 131 1 13 HELIX 9 9 LYS A 132 LEU A 136 5 5 HELIX 10 10 LYS A 141 ILE A 147 5 7 SHEET 1 AA 4 GLN A 31 MET A 38 0 SHEET 2 AA 4 VAL A 70 GLN A 76 -1 O VAL A 70 N MET A 38 SHEET 3 AA 4 LYS A 3 VAL A 8 -1 O THR A 4 N TRP A 75 SHEET 4 AA 4 ILE A 114 GLY A 116 -1 O HIS A 115 N MET A 7 CRYST1 107.531 107.531 52.301 90.00 90.00 120.00 P 63 2 2 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 0.009300 0.005369 0.000000 0.00000 SCALE2 0.000000 0.010738 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019120 0.00000 TER 1171 TYR A 148 HETATM 1172 O HOH A2001 -8.413 44.746 -7.940 1.00 23.01 O HETATM 1173 O HOH A2002 -15.403 42.208 -4.204 1.00 52.77 O HETATM 1174 O HOH A2003 -2.230 43.977 -4.027 1.00 20.31 O HETATM 1175 O HOH A2004 10.594 54.652 15.032 1.00 39.24 O HETATM 1176 O HOH A2005 -2.752 56.667 8.529 1.00 43.00 O HETATM 1177 O HOH A2006 9.151 44.717 -4.831 1.00 41.56 O HETATM 1178 O HOH A2007 6.017 61.057 6.017 1.00 37.08 O HETATM 1179 O HOH A2008 13.754 44.262 1.709 1.00 35.19 O HETATM 1180 O HOH A2009 13.797 50.724 14.933 1.00 51.24 O HETATM 1181 O HOH A2010 16.224 47.802 13.544 1.00 22.35 O HETATM 1182 O HOH A2011 17.004 50.489 10.954 0.50 37.11 O HETATM 1183 O HOH A2012 12.895 54.157 11.648 1.00 47.85 O HETATM 1184 O HOH A2013 14.081 50.474 4.086 1.00 19.72 O HETATM 1185 O HOH A2014 15.515 54.280 9.894 1.00 35.69 O HETATM 1186 O HOH A2015 8.205 53.750 14.518 1.00 37.26 O HETATM 1187 O HOH A2016 -0.419 55.426 9.299 1.00 42.23 O HETATM 1188 O HOH A2017 1.929 56.290 8.017 1.00 34.59 O HETATM 1189 O HOH A2018 4.187 59.636 6.677 1.00 49.59 O HETATM 1190 O HOH A2019 -9.007 46.612 11.923 1.00 18.93 O HETATM 1191 O HOH A2020 -4.993 52.135 13.278 1.00 17.20 O HETATM 1192 O HOH A2021 -11.873 53.247 9.005 1.00 33.77 O HETATM 1193 O HOH A2022 -10.802 49.408 8.420 1.00 32.11 O HETATM 1194 O HOH A2023 -13.587 46.959 6.365 1.00 39.35 O HETATM 1195 O HOH A2024 -14.277 43.745 3.893 1.00 46.93 O HETATM 1196 O HOH A2025 0.155 58.454 -6.221 1.00 38.01 O HETATM 1197 O HOH A2026 3.527 30.554 9.923 1.00 47.75 O HETATM 1198 O HOH A2027 4.194 35.402 15.137 1.00 22.08 O HETATM 1199 O HOH A2028 5.280 32.757 13.043 1.00 50.47 O HETATM 1200 O HOH A2029 0.000 62.080 -5.817 0.33 45.57 O HETATM 1201 O HOH A2030 0.000 62.085 2.534 0.33 40.10 O HETATM 1202 O HOH A2031 7.783 30.355 9.265 1.00 42.72 O HETATM 1203 O HOH A2032 8.116 31.802 11.580 1.00 36.50 O HETATM 1204 O HOH A2033 14.432 30.727 8.295 1.00 49.34 O HETATM 1205 O HOH A2034 18.972 46.377 -6.246 1.00 48.73 O HETATM 1206 O HOH A2035 20.669 49.562 -2.440 1.00 45.05 O HETATM 1207 O HOH A2036 12.020 24.737 5.762 1.00 45.89 O HETATM 1208 O HOH A2037 10.420 31.347 -3.906 1.00 39.81 O HETATM 1209 O HOH A2038 18.037 37.181 -2.760 1.00 50.68 O HETATM 1210 O HOH A2039 12.374 35.815 6.863 1.00 32.82 O HETATM 1211 O HOH A2040 13.238 41.884 9.796 1.00 25.71 O HETATM 1212 O HOH A2041 -10.910 49.727 -4.047 1.00 38.53 O HETATM 1213 O HOH A2042 -13.729 43.631 -5.953 1.00 31.03 O HETATM 1214 O HOH A2043 -3.072 49.152 -9.361 1.00 49.61 O HETATM 1215 O HOH A2044 -9.335 50.001 -7.980 1.00 53.39 O HETATM 1216 O HOH A2045 2.420 44.735 -7.240 1.00 37.68 O HETATM 1217 O HOH A2046 0.091 55.394 -6.486 1.00 28.25 O HETATM 1218 O HOH A2047 -0.638 54.837 1.348 1.00 22.90 O HETATM 1219 O HOH A2048 2.675 48.987 -6.814 1.00 44.73 O HETATM 1220 O HOH A2049 3.460 55.822 -7.204 1.00 19.70 O HETATM 1221 O HOH A2050 5.737 49.799 -10.442 1.00 49.57 O HETATM 1222 O HOH A2051 8.846 51.193 -10.398 1.00 40.96 O HETATM 1223 O HOH A2052 14.801 52.415 -9.887 1.00 64.30 O HETATM 1224 O HOH A2053 10.360 59.098 -4.034 1.00 38.39 O HETATM 1225 O HOH A2054 14.368 53.905 -6.085 1.00 33.22 O HETATM 1226 O HOH A2055 11.953 60.320 -6.297 1.00 36.15 O HETATM 1227 O HOH A2056 4.250 57.511 -9.511 1.00 45.81 O HETATM 1228 O HOH A2057 1.759 63.342 -4.054 1.00 22.93 O HETATM 1229 O HOH A2058 -1.238 58.840 2.231 1.00 30.78 O HETATM 1230 O HOH A2059 3.934 46.756 -6.413 1.00 56.66 O HETATM 1231 O HOH A2060 6.876 62.454 2.120 1.00 38.74 O HETATM 1232 O HOH A2061 8.277 60.964 4.173 1.00 19.21 O HETATM 1233 O HOH A2062 1.688 60.582 3.692 1.00 35.11 O HETATM 1234 O HOH A2063 17.109 52.055 -6.077 1.00 43.66 O HETATM 1235 O HOH A2064 13.417 44.762 -4.047 1.00 40.26 O HETATM 1236 O HOH A2065 18.603 48.984 -4.882 1.00 42.98 O HETATM 1237 O HOH A2066 15.141 52.166 1.055 1.00 18.39 O HETATM 1238 O HOH A2067 7.697 42.628 -4.140 1.00 37.92 O HETATM 1239 O HOH A2068 4.896 44.674 -4.686 1.00 22.77 O HETATM 1240 O HOH A2069 -1.143 43.204 -13.102 1.00 55.71 O HETATM 1241 O HOH A2070 -5.473 30.949 -1.725 1.00 40.11 O HETATM 1242 O HOH A2071 -7.147 30.974 -6.924 1.00 52.41 O HETATM 1243 O HOH A2072 2.746 39.354 -7.022 1.00 24.46 O HETATM 1244 O HOH A2073 -12.911 32.084 11.125 1.00 46.57 O HETATM 1245 O HOH A2074 -18.046 38.522 13.555 1.00 42.98 O HETATM 1246 O HOH A2075 -10.054 45.089 10.041 1.00 26.30 O HETATM 1247 O HOH A2076 -18.656 42.435 7.301 1.00 50.11 O HETATM 1248 O HOH A2077 -18.055 51.207 13.540 0.50 12.66 O HETATM 1249 O HOH A2078 -25.655 53.015 6.134 1.00 45.82 O HETATM 1250 O HOH A2079 -26.081 53.987 11.673 1.00 48.83 O HETATM 1251 O HOH A2080 -13.490 46.179 3.152 1.00 32.26 O MASTER 370 0 0 10 4 0 0 6 1250 1 0 12 END