PDB Short entry for 2X1J HEADER OXIDOREDUCTASE 07-JAN-10 2X1J TITLE H71A MUTANT OF THE ANTIBIOTIC RESISTANCE PROTEIN NIMA FROM DEINOCOCCUS TITLE 2 RADIODURANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NIMA-RELATED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 5-NITROIMIDAZOLE REDUCTASE, NIMA REDUCTASE; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES 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 STAR(DE3)PLYSS KEYWDS ANTIBIOTIC RESISTANCE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR H.S.LEIROS,B.O.BRANDSDAL,S.M.MCSWEENEY REVDAT 2 20-DEC-23 2X1J 1 REMARK REVDAT 1 17-NOV-10 2X1J 0 JRNL AUTH H.S.LEIROS,B.O.BRANDSDAL,S.M.MCSWEENEY JRNL TITL BIOPHYSICAL CHARACTERIZATION AND MUTATIONAL ANALYSIS OF THE JRNL TITL 2 ANTIBIOTIC RESISTANCE PROTEIN NIMA FROM DEINOCOCCUS JRNL TITL 3 RADIODURANS. JRNL REF BIOCHIM.BIOPHYS.ACTA V.1804 967 2010 JRNL REFN ISSN 0006-3002 JRNL PMID 20096385 JRNL DOI 10.1016/J.BBAPAP.2010.01.010 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. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0069 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 84.9 REMARK 3 NUMBER OF REFLECTIONS : 13599 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 720 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 895 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.93 REMARK 3 BIN R VALUE (WORKING SET) : 0.2530 REMARK 3 BIN FREE R VALUE SET COUNT : 48 REMARK 3 BIN FREE R VALUE : 0.2600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1632 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 231 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.26000 REMARK 3 B22 (A**2) : -0.14000 REMARK 3 B33 (A**2) : -0.37000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.93000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.219 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.195 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.119 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.024 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.926 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.865 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1667 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1137 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2270 ; 1.479 ; 1.942 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2734 ; 1.700 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 202 ; 6.623 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 84 ;32.783 ;22.976 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 253 ;15.317 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;16.643 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 240 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1883 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 359 ; 0.001 ; 0.020 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): 1019 ; 0.664 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 408 ; 0.160 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1634 ; 1.154 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 648 ; 1.698 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 636 ; 2.553 ; 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 2X1J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-JAN-10. REMARK 100 THE DEPOSITION ID IS D_1290042327. 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 : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9333 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14356 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 86.6 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 0.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.14000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.700 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 (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10MG/ML PROTEIN, 0.6M SODIUM ACETATE, REMARK 280 0.1M BUFFER PH 6 (CITRATE/MES). 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 50.12700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.48100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.12700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.48100 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: 4480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.1 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 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 A2158 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, HIS 71 TO ALA 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 LEU 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 ARG A 21 NH1 NH2 REMARK 480 GLU A 147 CG CD OE1 OE2 REMARK 480 LYS A 158 CD CE NZ REMARK 480 ARG A 159 CZ NH1 NH2 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 2161 O HOH A 2163 0.66 REMARK 500 O HOH A 2143 O HOH A 2144 1.97 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 2029 O HOH A 2113 3555 2.16 REMARK 500 CG2 VAL A 75 O HOH A 2024 3445 2.18 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 ARG A 21 CZ ARG A 21 NH1 0.117 REMARK 500 LYS A 158 CG LYS A 158 CD -0.287 REMARK 500 LYS A 158 CE LYS A 158 NZ -0.208 REMARK 500 ARG A 159 NE ARG A 159 CZ 0.121 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 21 NH1 - CZ - NH2 ANGL. DEV. = -6.8 DEGREES REMARK 500 LYS A 158 CB - CG - CD ANGL. DEV. = 41.2 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 3 -10.45 -41.18 REMARK 500 ARG A 77 -78.93 -85.93 REMARK 500 GLU A 147 -73.47 -119.78 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 ARG A 21 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. 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 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: 2VPA RELATED DB: PDB REMARK 900 HIGH RESOLUTION CRYSTAL STRUCTURE OF THE ANTIBIOTIC RESISTANCE REMARK 900 PROTEIN NIMA FROM DEINOCOCCUS RADIODURANS 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 900 RELATED ID: 2X1K RELATED DB: PDB REMARK 900 H71S MUTANT OF THE ANTIBIOTIC RESISTANCE PROTEIN NIMA FROM REMARK 900 DEINOCOCCUS RADIODURANS DBREF 2X1J A 2 195 UNP Q9RW27 Q9RW27_DEIRA 2 195 SEQADV 2X1J MET A -20 UNP Q9RW27 EXPRESSION TAG SEQADV 2X1J SER A -19 UNP Q9RW27 EXPRESSION TAG SEQADV 2X1J TYR A -18 UNP Q9RW27 EXPRESSION TAG SEQADV 2X1J TYR A -17 UNP Q9RW27 EXPRESSION TAG SEQADV 2X1J HIS A -16 UNP Q9RW27 EXPRESSION TAG SEQADV 2X1J HIS A -15 UNP Q9RW27 EXPRESSION TAG SEQADV 2X1J HIS A -14 UNP Q9RW27 EXPRESSION TAG SEQADV 2X1J HIS A -13 UNP Q9RW27 EXPRESSION TAG SEQADV 2X1J HIS A -12 UNP Q9RW27 EXPRESSION TAG SEQADV 2X1J HIS A -11 UNP Q9RW27 EXPRESSION TAG SEQADV 2X1J LEU A -10 UNP Q9RW27 EXPRESSION TAG SEQADV 2X1J GLU A -9 UNP Q9RW27 EXPRESSION TAG SEQADV 2X1J SER A -8 UNP Q9RW27 EXPRESSION TAG SEQADV 2X1J THR A -7 UNP Q9RW27 EXPRESSION TAG SEQADV 2X1J SER A -6 UNP Q9RW27 EXPRESSION TAG SEQADV 2X1J LEU A -5 UNP Q9RW27 EXPRESSION TAG SEQADV 2X1J TYR A -4 UNP Q9RW27 EXPRESSION TAG SEQADV 2X1J LYS A -3 UNP Q9RW27 EXPRESSION TAG SEQADV 2X1J LYS A -2 UNP Q9RW27 EXPRESSION TAG SEQADV 2X1J ALA A -1 UNP Q9RW27 EXPRESSION TAG SEQADV 2X1J GLY A 0 UNP Q9RW27 EXPRESSION TAG SEQADV 2X1J LEU A 1 UNP Q9RW27 EXPRESSION TAG SEQADV 2X1J ALA A 71 UNP Q9RW27 HIS 71 ENGINEERED MUTATION 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 LEU 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 ALA 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 HETNAM ACT ACETATE ION FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 HOH *231(H2 O) HELIX 1 1 SER A -19 LEU A -10 1 10 HELIX 2 2 SER A 23 GLY A 34 1 12 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 ILE A 36 GLN A 44 0 SHEET 2 AA 7 ALA A 50 ARG A 62 -1 O PHE A 51 N TRP A 43 SHEET 3 AA 7 ASP A 67 ALA A 71 -1 O ASP A 67 N ARG A 62 SHEET 4 AA 7 VAL A 162 ASN A 175 -1 O TYR A 163 N TYR A 70 SHEET 5 AA 7 SER A 108 VAL A 122 -1 O TYR A 111 N ASN A 175 SHEET 6 AA 7 HIS A 86 LEU A 99 -1 O HIS A 86 N ALA A 120 SHEET 7 AA 7 ILE A 36 GLN A 44 -1 O ARG A 38 N GLU A 91 SITE 1 AC1 4 THR A 41 TYR A 70 ARG A 79 HIS A 86 CRYST1 100.254 38.962 60.080 90.00 113.99 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 0.009975 0.000000 0.004439 0.00000 SCALE2 0.000000 0.025666 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018218 0.00000