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- PDB-1w3o: Crystal structure of NimA from D. radiodurans -

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Basic information

Entry
Database: PDB / ID: 1w3o
TitleCrystal structure of NimA from D. radiodurans
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
ACETATE ION / PYRUVIC ACID / NimA-related protein
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.6 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: Atomic model / Data collection ...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
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

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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)24,6143
Polymers24,4671
Non-polymers1472
Water5,999333
1
A: NIMA-RELATED PROTEIN
hetero molecules

A: NIMA-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2296
Polymers48,9342
Non-polymers2944
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)99.863, 38.947, 59.811
Angle α, β, γ (deg.)90.00, 114.25, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2102-

HOH

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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 %
Crystal growDetails: 0.65-0.9 M SODIUM ACETATE, AND 0.1 M CACODYLATE, CITRATE OR MES BUFFERED AT PH 5.5-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 26056 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.2
Reflection shellRedundancy: 3.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.6→19.46 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.145 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1326 5.1 %RANDOM
Rwork0.162 ---
obs0.164 24728 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0.04 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1637 0 10 333 1980
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0211678
X-RAY DIFFRACTIONr_bond_other_d0.0030.021474
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.9342284
X-RAY DIFFRACTIONr_angle_other_deg0.90533409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7175202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1140.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021897
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02361
X-RAY DIFFRACTIONr_nbd_refined0.220.2298
X-RAY DIFFRACTIONr_nbd_other0.2630.21680
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0890.2994
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2250.2227
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2950.2166
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.239
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1381.51019
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.89621635
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6093659
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9154.5649
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: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.273 77
Rwork0.272 1629

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