PDB Short entry for 1W3R HEADER ANTIBIOTIC RESISTANCE 17-JUL-04 1W3R TITLE NIMA FROM D. RADIODURANS WITH METRONIDAZOLE AND PYRUVATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NIMA-RELATED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 5-NITROIMIDAZOLE ANTIBIOTIC RESISTANCE PROTEIN; COMPND 5 ENGINEERED: 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(DE3) KEYWDS ANTIBIOTIC RESISTANCE, DEINOCOCCUS RADIODURANS, 5-NITROIMIDAZOLE KEYWDS 2 RESISTANCE, NIM GENE, CATALYTIC MECHANISM EXPDTA X-RAY DIFFRACTION AUTHOR H.-K.S.LEIROS,S.KOZIELSKI-STUHRMANN,U.KAPP,L.TERRADOT,G.A.LEONARD, AUTHOR 2 S.M.MCSWEENEY REVDAT 6 13-DEC-23 1W3R 1 REMARK REVDAT 5 15-NOV-23 1W3R 1 REMARK ATOM REVDAT 4 29-MAR-17 1W3R 1 DBREF SEQADV HETNAM HETSYN REVDAT 3 24-FEB-09 1W3R 1 VERSN REVDAT 2 06-JAN-05 1W3R 1 JRNL REVDAT 1 18-OCT-04 1W3R 0 JRNL AUTH H.-K.S.LEIROS,S.KOZIELSKI-STUHRMANN,U.KAPP,L.TERRADOT, JRNL AUTH 2 G.A.LEONARD,S.M.MCSWEENEY JRNL TITL STRUCTURAL BASIS OF 5-NITROIMIDAZOLE ANTIBIOTIC RESISTANCE: JRNL TITL 2 THE CRYSTAL STRUCTURE OF NIMA FROM DEINOCOCCUS RADIODURANS JRNL REF J.BIOL.CHEM. V. 279 55840 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 15492014 JRNL DOI 10.1074/JBC.M408044200 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0003 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 (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 15992 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 852 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) : 1160 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2890 REMARK 3 BIN FREE R VALUE SET COUNT : 61 REMARK 3 BIN FREE R VALUE : 0.3570 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 : 22 REMARK 3 SOLVENT ATOMS : 293 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.26000 REMARK 3 B22 (A**2) : 0.47000 REMARK 3 B33 (A**2) : -1.31000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.74000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.177 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.172 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.138 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.781 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.890 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1683 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2289 ; 1.476 ; 1.934 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 202 ; 7.075 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 84 ;35.796 ;22.976 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 253 ;14.780 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;13.402 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 239 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1334 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 708 ; 0.207 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1131 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 228 ; 0.182 ; 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): 140 ; 0.215 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 48 ; 0.149 ; 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): 1043 ; 0.923 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1632 ; 1.457 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 746 ; 2.072 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 657 ; 3.099 ; 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 : BABINET MODEL WITH 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 1W3R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-JUL-04. REMARK 100 THE DEPOSITION ID IS D_1290020499. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.939 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16846 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.3000 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.38000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.900 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: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 49.79600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.58300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 49.79600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.58300 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: PQS 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 -21 REMARK 465 GLU A -10 REMARK 465 SER A -9 REMARK 465 THR A -8 REMARK 465 SER A -7 REMARK 465 LEU A -6 REMARK 465 TYR A -5 REMARK 465 LYS A -4 REMARK 465 LYS A -3 REMARK 465 ALA A -2 REMARK 465 GLY A -1 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 HIS A -13 CB CG ND1 CD2 CE1 NE2 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 NH2 ARG A 21 O HOH A 2068 1.93 REMARK 500 O HOH A 2216 O HOH A 2219 2.08 REMARK 500 NE2 HIS A 71 O PYR A 1197 2.12 REMARK 500 OE2 GLU A 91 OG SER A 93 2.16 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 HIS A -13 CA HIS A -13 CB -0.151 REMARK 500 ARG A 21 CZ ARG A 21 NH1 0.931 REMARK 500 ARG A 21 CZ ARG A 21 NH2 0.581 REMARK 500 LYS A 158 CE LYS A 158 NZ -0.217 REMARK 500 ARG A 159 NE ARG A 159 CZ -0.172 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. = -53.1 DEGREES REMARK 500 ARG A 21 NE - CZ - NH1 ANGL. DEV. = -35.4 DEGREES REMARK 500 ARG A 21 NE - CZ - NH2 ANGL. DEV. = -25.6 DEGREES REMARK 500 LYS A 158 CB - CG - CD ANGL. DEV. = 30.8 DEGREES REMARK 500 ARG A 159 CD - NE - CZ ANGL. DEV. = 25.5 DEGREES REMARK 500 ARG A 159 NE - CZ - NH1 ANGL. DEV. = -35.0 DEGREES REMARK 500 ARG A 159 NE - CZ - NH2 ANGL. DEV. = 27.6 DEGREES REMARK 500 ASP A 185 CB - CG - OD2 ANGL. DEV. = 5.9 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 -56.87 -11.95 REMARK 500 ARG A 77 -89.83 -78.75 REMARK 500 GLU A 147 -66.26 -129.47 REMARK 500 PRO A 187 127.05 -39.84 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 0.41 SIDE CHAIN REMARK 500 ARG A 159 0.13 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 A2051 DISTANCE = 6.48 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 A1196 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PYR A1197 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2MN A1198 REMARK 900 REMARK 900 RELATED ENTRIES 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 CRYSTAL STRUCTURE OF NIMA FROM D. RADIODURANS REMARK 900 RELATED ID: 1W3Q RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NIMA FROM D. RADIODURANS DBREF 1W3R A 1 195 UNP Q9RW27 Q9RW27_DEIRA 1 195 SEQADV 1W3R MET A -21 UNP Q9RW27 EXPRESSION TAG SEQADV 1W3R SER A -20 UNP Q9RW27 EXPRESSION TAG SEQADV 1W3R TYR A -19 UNP Q9RW27 EXPRESSION TAG SEQADV 1W3R TYR A -18 UNP Q9RW27 EXPRESSION TAG SEQADV 1W3R HIS A -17 UNP Q9RW27 EXPRESSION TAG SEQADV 1W3R HIS A -16 UNP Q9RW27 EXPRESSION TAG SEQADV 1W3R HIS A -15 UNP Q9RW27 EXPRESSION TAG SEQADV 1W3R HIS A -14 UNP Q9RW27 EXPRESSION TAG SEQADV 1W3R HIS A -13 UNP Q9RW27 EXPRESSION TAG SEQADV 1W3R HIS A -12 UNP Q9RW27 EXPRESSION TAG SEQADV 1W3R LEU A -11 UNP Q9RW27 EXPRESSION TAG SEQADV 1W3R GLU A -10 UNP Q9RW27 EXPRESSION TAG SEQADV 1W3R SER A -9 UNP Q9RW27 EXPRESSION TAG SEQADV 1W3R THR A -8 UNP Q9RW27 EXPRESSION TAG SEQADV 1W3R SER A -7 UNP Q9RW27 EXPRESSION TAG SEQADV 1W3R LEU A -6 UNP Q9RW27 EXPRESSION TAG SEQADV 1W3R TYR A -5 UNP Q9RW27 EXPRESSION TAG SEQADV 1W3R LYS A -4 UNP Q9RW27 EXPRESSION TAG SEQADV 1W3R LYS A -3 UNP Q9RW27 EXPRESSION TAG SEQADV 1W3R ALA A -2 UNP Q9RW27 EXPRESSION TAG SEQADV 1W3R GLY A -1 UNP Q9RW27 EXPRESSION TAG 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 HET 2MN A1198 12 HETNAM ACT ACETATE ION HETNAM PYR PYRUVIC ACID HETNAM 2MN METRONIDAZOLE FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 PYR C3 H4 O3 FORMUL 4 2MN C6 H9 N3 O3 FORMUL 5 HOH *293(H2 O) HELIX 1 1 SER A 2 ASP A 6 5 5 HELIX 2 2 SER A 23 GLY A 34 1 12 HELIX 3 3 SER A 103 LEU A 107 5 5 HELIX 4 4 ALA A 124 PHE A 140 1 17 HELIX 5 5 SER A 153 ARG A 159 1 7 HELIX 6 6 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 6 THR A 41 TYR A 70 THR A 72 ARG A 79 SITE 2 AC1 6 HIS A 86 HOH A2151 SITE 1 AC2 7 HIS A 71 PHE A 98 LEU A 107 VAL A 139 SITE 2 AC2 7 HOH A2289 HOH A2290 HOH A2291 SITE 1 AC3 9 THR A 55 PRO A 56 VAL A 109 TYR A 111 SITE 2 AC3 9 SER A 113 LYS A 173 HOH A2149 HOH A2259 SITE 3 AC3 9 HOH A2293 CRYST1 99.592 39.166 59.836 90.00 114.09 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 0.010041 0.000000 0.004490 0.00000 SCALE2 0.000000 0.025532 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018307 0.00000