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- PDB-1w3q: NimA from D. radiodurans with covalenly bound lactate -

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Basic information

Entry
Database: PDB / ID: 1w3q
TitleNimA from D. radiodurans with covalenly bound lactate
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 / LACTIC ACID / NimA-related protein
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id
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)24,6163
Polymers24,4671
Non-polymers1492
Water4,864270
1
A: NIMA-RELATED PROTEIN
hetero molecules

A: NIMA-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2336
Polymers48,9342
Non-polymers2984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)99.803, 38.773, 60.001
Angle α, β, γ (deg.)90.00, 114.05, 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
Details: COVALENT LINK FROM HIS71 TO A LACTATE MOLECULE
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RW27
#2: Chemical ChemComp-LAC / LACTIC ACID


Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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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: 1.88→30 Å / Num. obs: 17262 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.9
Reflection shellRedundancy: 2.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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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: 1.88→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.794 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 878 5.1 %RANDOM
Rwork0.169 ---
obs0.172 16383 99.8 %-
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: 21.56 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20 Å21.3 Å2
2--0.15 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.88→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1637 0 10 270 1917
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211677
X-RAY DIFFRACTIONr_bond_other_d0.0020.021481
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.9322285
X-RAY DIFFRACTIONr_angle_other_deg0.8273.0013408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8815202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61322.97684
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67615252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6191516
X-RAY DIFFRACTIONr_chiral_restr0.0940.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021891
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02358
X-RAY DIFFRACTIONr_nbd_refined0.2010.2292
X-RAY DIFFRACTIONr_nbd_other0.1980.21406
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2776
X-RAY DIFFRACTIONr_nbtor_other0.0880.2983
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.2194
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2260.2131
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.191.51289
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.44721635
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1913774
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0064.5650
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: 1.88→1.93 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.262 66
Rwork0.256 1202

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