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- PDB-1w3r: NimA from D. radiodurans with Metronidazole and Pyruvate -

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Basic information

Entry
Database: PDB / ID: 1w3r
TitleNimA from D. radiodurans with Metronidazole and Pyruvate
ComponentsNIMA-RELATED PROTEIN
KeywordsANTIBIOTIC RESISTANCE / DEINOCOCCUS RADIODURANS / 5-NITROIMIDAZOLE RESISTANCE / NIM GENE / CATALYTIC MECHANISM
Function / homology
Function and homology information


Pyridoxamine 5'-phosphate oxidase-related / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
Metronidazole / ACETATE ION / PYRUVIC ACID / NimA-related protein
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLeiros, H.-K.S. / Kozielski-Stuhrmann, S. / Kapp, U. / Terradot, L. / Leonard, G.A. / McSweeney, S.M.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural Basis of 5-Nitroimidazole Antibiotic Resistance: The Crystal Structure of Nima from Deinococcus Radiodurans
Authors: Leiros, H.-K.S. / Kozielski-Stuhrmann, S. / Kapp, U. / Terradot, L. / Leonard, G.A. / Mcsweeney, S.M.
History
DepositionJul 17, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2004Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_validate_close_contact
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_validate_close_contact.auth_atom_id_2
Revision 2.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NIMA-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7854
Polymers24,4671
Non-polymers3183
Water5,278293
1
A: NIMA-RELATED PROTEIN
hetero molecules

A: NIMA-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5718
Polymers48,9342
Non-polymers6376
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)99.592, 39.166, 59.836
Angle α, β, γ (deg.)90.00, 114.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein NIMA-RELATED PROTEIN / 5-NITROIMIDAZOLE ANTIBIOTIC RESISTANCE PROTEIN


Mass: 24467.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RW27
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3
#4: Chemical ChemComp-2MN / Metronidazole


Mass: 171.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9N3O3 / Comment: medication, antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 16846 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.3
Reflection shellRedundancy: 4.4 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W3O

1w3o


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.89 / SU B: 4.781 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 852 5.1 %RANDOM
Rwork0.189 ---
obs0.192 15992 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.26 Å20 Å21.74 Å2
2--0.47 Å20 Å2
3----1.31 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1637 0 22 293 1952
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211683
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.9342289
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0755202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79622.97684
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7815253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4021517
X-RAY DIFFRACTIONr_chiral_restr0.110.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021334
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.2708
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21131
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2228
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.2140
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.248
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9231.51043
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.45721632
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0723746
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0994.5657
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.357 61
Rwork0.289 1160

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