HEADER OXIDOREDUCTASE 27-FEB-08 2VPA TITLE HIGH RESOLUTION CRYSTAL STRUCTURE OF THE ANTIBIOTIC RESISTANCE PROTEIN TITLE 2 NIMA FROM DEINOCOCCUS RADIODURANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NIMA-RELATED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 5-NITROIMIDAZOLE REDUCTASE; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: INCLUDES THE FIRST 10 RESIDUES OF THE 21 RESIDUE LONG COMPND 7 N-TERMINAL HIS TAG SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DEINOCOCCUS RADIODURANS; SOURCE 3 ORGANISM_TAXID: 1299; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLYSS KEYWDS COFACTOR, ATOMIC RESOLUTION, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR H.-K.S.LEIROS,C.TEDESCO,S.M.MCSWEENEY REVDAT 6 13-DEC-23 2VPA 1 REMARK REVDAT 5 15-NOV-23 2VPA 1 REMARK ATOM REVDAT 4 30-JAN-13 2VPA 1 KEYWDS JRNL REMARK VERSN REVDAT 4 2 1 FORMUL REVDAT 3 24-FEB-09 2VPA 1 VERSN REVDAT 2 09-SEP-08 2VPA 1 SOURCE JRNL REVDAT 1 19-AUG-08 2VPA 0 JRNL AUTH H.-K.S.LEIROS,C.TEDESCO,S.M.MCSWEENEY JRNL TITL HIGH-RESOLUTION STRUCTURE OF THE ANTIBIOTIC RESISTANCE JRNL TITL 2 PROTEIN NIMA FROM DEINOCOCCUS RADIODURANS. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 64 442 2008 JRNL REFN ESSN 1744-3091 JRNL PMID 18540048 JRNL DOI 10.1107/S1744309108009901 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.-K.S.LEIROS,S.KOZIELSKI-STUHRMANN,U.KAPP,L.TERRADOT, REMARK 1 AUTH 2 G.A.LEONARD,S.M.MCSWEENEY REMARK 1 TITL STRUCTURAL BASIS OF 5-NITROIMIDAZOLE ANTIBIOTIC RESISTANCE: REMARK 1 TITL 2 THE CRYSTAL STRUCTURE OF NIMA FROM DEINOCOCCUS RADIODURANS REMARK 1 REF J.BIOL.CHEM. V. 279 55840 2004 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 15492014 REMARK 1 DOI 10.1074/JBC.M408044200 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0021 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 63865 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) : 0.142 REMARK 3 R VALUE (WORKING SET) : 0.141 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2004 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) : 1.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.23 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4633 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2550 REMARK 3 BIN FREE R VALUE SET COUNT : 158 REMARK 3 BIN FREE R VALUE : 0.3370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1637 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 406 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.16 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.34000 REMARK 3 B22 (A**2) : -0.05000 REMARK 3 B33 (A**2) : -0.12000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.20000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.038 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.040 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.025 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.228 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.963 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1806 ; 0.020 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1231 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2475 ; 1.734 ; 1.939 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2961 ; 1.012 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 227 ; 6.775 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 95 ;35.342 ;22.737 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 275 ;12.756 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;13.977 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 255 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2116 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 406 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 335 ; 0.245 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1331 ; 0.223 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 870 ; 0.183 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 997 ; 0.091 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 292 ; 0.258 ; 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): 22 ; 0.113 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 114 ; 0.252 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 62 ; 0.223 ; 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): 1389 ; 2.125 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1777 ; 2.607 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 830 ; 3.476 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 698 ; 4.359 ; 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 : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2VPA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-FEB-08. REMARK 100 THE DEPOSITION ID IS D_1290035469. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9999 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 : NULL REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65888 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.61000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1W3O REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.6-0.7 M SODIUM ACETATE AND 0.1 M MES REMARK 280 PH 6 OR 0.1 M NA CACODYLATE PH 6.5. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 50.01850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.47550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.01850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.47550 REMARK 290 SMTRY3 4 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: 5770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.3 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 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 MET A -20 REMARK 465 GLU A -9 REMARK 465 SER A -8 REMARK 465 THR A -7 REMARK 465 SER A -6 REMARK 465 LEU A -5 REMARK 465 TYR A -4 REMARK 465 LYS A -3 REMARK 465 LYS A -2 REMARK 465 ALA A -1 REMARK 465 GLY A 0 REMARK 465 MET A 1 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 GLU A 29 OE1 REMARK 480 GLU A 46 CD OE2 REMARK 480 GLU A 147 CD REMARK 480 LYS A 158 CD CE NZ 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 O HOH A 2159 O HOH A 2161 1.85 REMARK 500 O HOH A 2108 O HOH A 2355 1.87 REMARK 500 OE1 GLU A 29 O HOH A 2138 1.89 REMARK 500 O HOH A 2082 O HOH A 2083 1.95 REMARK 500 OG1 THR A 41 O HOH A 2165 1.97 REMARK 500 O HOH A 2234 O HOH A 2236 1.98 REMARK 500 OXT PYR A 1197 O HOH A 2406 1.99 REMARK 500 OE1 GLU A 29 O HOH A 2136 2.07 REMARK 500 O HOH A 2403 O HOH A 2406 2.12 REMARK 500 O HOH A 2231 O HOH A 2233 2.13 REMARK 500 O HOH A 2230 O HOH A 2231 2.15 REMARK 500 OG SER A 108 O HOH A 2265 2.18 REMARK 500 O HOH A 2165 O HOH A 2166 2.19 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 O HOH A 2264 O HOH A 2406 2555 1.77 REMARK 500 O HOH A 2261 O HOH A 2403 2555 1.89 REMARK 500 O HOH A 2290 O HOH A 2290 2556 1.98 REMARK 500 CA GLY A 83 O HOH A 2314 1545 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 GLU A 29 CD GLU A 29 OE1 -0.079 REMARK 500 ARG A 33 CG ARG A 33 CD 0.160 REMARK 500 ARG A 38 CG ARG A 38 CD -0.182 REMARK 500 GLU A 46 CD GLU A 46 OE1 0.238 REMARK 500 GLU A 147 CG GLU A 147 CD 0.239 REMARK 500 GLU A 147 CD GLU A 147 OE1 0.702 REMARK 500 GLU A 147 CD GLU A 147 OE2 0.358 REMARK 500 LYS A 158 CE LYS A 158 NZ -0.218 REMARK 500 TRP A 193 CB TRP A 193 CG -0.139 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 A 10 NE - CZ - NH1 ANGL. DEV. = 5.9 DEGREES REMARK 500 GLU A 29 OE1 - CD - OE2 ANGL. DEV. = -8.9 DEGREES REMARK 500 ARG A 121 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 138 NE - CZ - NH2 ANGL. DEV. = -5.5 DEGREES REMARK 500 GLU A 147 CB - CG - CD ANGL. DEV. = -21.8 DEGREES REMARK 500 GLU A 147 OE1 - CD - OE2 ANGL. DEV. = -21.3 DEGREES REMARK 500 LYS A 158 CB - CG - CD ANGL. DEV. = 18.5 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 ARG A 77 -79.28 -91.39 REMARK 500 ASN A 81 161.95 170.53 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 GLU A 29 0.08 SIDE CHAIN 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 A2010 DISTANCE = 6.58 ANGSTROMS REMARK 525 HOH A2014 DISTANCE = 6.47 ANGSTROMS REMARK 525 HOH A2043 DISTANCE = 6.16 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1196 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PYR A 1197 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1W3Q RELATED DB: PDB REMARK 900 NIMA FROM D. RADIODURANS WITH COVALENLY BOUND LACTATE REMARK 900 RELATED ID: 1W3O RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NIMA FROM D. RADIODURANS REMARK 900 RELATED ID: 1W3P RELATED DB: PDB REMARK 900 NIMA FROM D. RADIODURANS WITH A HIS71- PYRUVATE RESIDUE REMARK 900 RELATED ID: 1W3R RELATED DB: PDB REMARK 900 NIMA FROM D. RADIODURANS WITH METRONIDAZOLE AND PYRUVATE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE VECTOR PDEST17 (INVITROGEN) WITH A 21 RESIDUE LONG HIS- REMARK 999 TAG (MSYYHHHHHHLESTSLYKKAG) IS ATTACHED TO THE PROTEIN DBREF 2VPA A -20 0 PDB 2VPA 2VPA -20 0 DBREF 2VPA A 1 195 UNP Q9RW27 Q9RW27_DEIRA 1 195 SEQRES 1 A 216 MET SER TYR TYR HIS HIS HIS HIS HIS HIS LEU GLU SER SEQRES 2 A 216 THR SER LEU TYR LYS LYS ALA GLY MET SER ASP PHE TYR SEQRES 3 A 216 ASP PRO ARG GLU ARG ASP PRO SER VAL SER ARG ARG PRO SEQRES 4 A 216 GLN ASN ARG GLN SER ASP GLU TRP ILE ARG GLU LEU LEU SEQRES 5 A 216 LEU ARG GLY THR ILE ALA ARG VAL ALA THR LEU TRP GLN SEQRES 6 A 216 GLY GLU ASP GLY ALA ALA PHE PRO PHE ILE THR PRO LEU SEQRES 7 A 216 ALA TYR ALA TYR ARG PRO GLU GLN GLY ASP LEU VAL TYR SEQRES 8 A 216 HIS THR ASN VAL VAL GLY ARG LEU ARG ALA ASN ALA GLY SEQRES 9 A 216 GLN GLY HIS PRO ALA THR LEU GLU VAL SER GLU ILE GLY SEQRES 10 A 216 GLN PHE LEU PRO SER ASN SER PRO LEU GLU LEU SER VAL SEQRES 11 A 216 GLN TYR ARG SER VAL MET VAL PHE GLY THR ALA ARG VAL SEQRES 12 A 216 LEU ALA GLY GLU ASP ALA ARG ALA ALA LEU THR THR LEU SEQRES 13 A 216 SER GLU ARG VAL PHE PRO GLY LEU LYS VAL GLY GLU THR SEQRES 14 A 216 THR ARG PRO ILE SER GLU ASP ASP LEU LYS ARG THR SER SEQRES 15 A 216 VAL TYR SER LEU SER ILE ASP ARG TRP SER GLY LYS GLU SEQRES 16 A 216 ASN TRP ALA GLU GLN ALA ILE GLN GLU GLU ASP TRP PRO SEQRES 17 A 216 ALA LEU GLY PRO GLU TRP LEU GLY HET ACT A1196 4 HET PYR A1197 6 HETNAM ACT ACETATE ION HETNAM PYR PYRUVIC ACID FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 PYR C3 H4 O3 FORMUL 4 HOH *406(H2 O) HELIX 1 1 SER A 23 GLY A 34 1 12 HELIX 2 2 SER A 103 LEU A 107 5 5 HELIX 3 3 ALA A 124 PHE A 140 1 17 HELIX 4 4 SER A 153 ARG A 159 1 7 HELIX 5 5 GLY A 190 GLY A 195 1 6 SHEET 1 AA 7 ALA A 50 ALA A 58 0 SHEET 2 AA 7 ILE A 36 GLN A 44 -1 O ALA A 37 N LEU A 57 SHEET 3 AA 7 HIS A 86 LEU A 99 -1 O THR A 89 N ALA A 40 SHEET 4 AA 7 SER A 108 VAL A 122 -1 O SER A 108 N LEU A 99 SHEET 5 AA 7 VAL A 162 ASN A 175 -1 O SER A 164 N ARG A 121 SHEET 6 AA 7 ASP A 67 HIS A 71 -1 O LEU A 68 N LEU A 165 SHEET 7 AA 7 ALA A 60 ARG A 62 -1 O ALA A 60 N VAL A 69 SITE 1 AC1 5 THR A 41 TYR A 70 ARG A 79 HIS A 86 SITE 2 AC1 5 HOH A2219 SITE 1 AC2 9 HIS A 71 PHE A 98 LEU A 107 SER A 108 SITE 2 AC2 9 HOH A2402 HOH A2403 HOH A2404 HOH A2405 SITE 3 AC2 9 HOH A2406 CRYST1 100.037 38.951 59.897 90.00 114.36 90.00 C 1 2 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 0.009996 0.000000 0.004526 0.00000 SCALE2 0.000000 0.025673 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018327 0.00000