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- PDB-7t2z: The structure of Haemophilus influenzae Rd KW20 nitroreductase co... -

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Basic information

Entry
Database: PDB / ID: 7t2z
TitleThe structure of Haemophilus influenzae Rd KW20 nitroreductase complexed with 1-methyl-5-nitroimidazole
ComponentsPutative NAD(P)H nitroreductase
KeywordsOXIDOREDUCTASE / Nitroreductase / Haemophilus influenzae / 1-methyl-5-nitroimidazole
Function / homology
Function and homology information


2,4,6-trinitrotoluene catabolic process / Oxidoreductases / oxidoreductase activity / cytosol
Similarity search - Function
Oxygen-insensitive NAD(P)H nitroreductase NfsB-like / : / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / 1-methyl-5-nitro-1H-imidazole / FLAVIN MONONUCLEOTIDE / Putative NAD(P)H nitroreductase
Similarity search - Component
Biological speciesHaemophilus influenzae Rd KW20 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2547 Å
AuthorsWanniarachchi, T.N. / Bruner, S.D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Rsc Chem Biol / Year: 2022
Title: Biochemical and structural characterization of Haemophilus influenzae nitroreductase in metabolizing nitroimidazoles.
Authors: Liu, D. / Wanniarachchi, T.N. / Jiang, G. / Seabra, G. / Cao, S. / Bruner, S.D. / Ding, Y.
History
DepositionDec 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative NAD(P)H nitroreductase
B: Putative NAD(P)H nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7198
Polymers53,4952
Non-polymers1,2246
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10840 Å2
ΔGint-47 kcal/mol
Surface area17100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.315, 57.315, 121.007
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative NAD(P)H nitroreductase


Mass: 26747.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae Rd KW20 (bacteria)
Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: HI_1278 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q57431, Oxidoreductases

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Non-polymers , 5 types, 91 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-EIV / 1-methyl-5-nitro-1H-imidazole


Mass: 127.101 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5N3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.68 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 8% v/v tacsimateTM pH 5.0 and 20% w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.2547→49.6481 Å / Num. obs: 20949 / % possible obs: 99.9 % / Redundancy: 5.2 % / CC1/2: 0.976 / CC star: 0.994 / Net I/σ(I): 7.82
Reflection shellResolution: 2.2547→2.3736 Å / Redundancy: 5 % / Num. unique obs: 2086 / CC1/2: 0.636 / CC star: 0.882 / % possible all: 99.05

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WT2

6wt2


Resolution: 2.2547→49.6481 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 24.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2224 970 4.63 %RANDOM
Rwork0.1784 19980 --
obs0.1804 20949 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.71 Å2 / Biso mean: 46.2929 Å2 / Biso min: 22.95 Å2
Refinement stepCycle: final / Resolution: 2.2547→49.6481 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3516 0 83 85 3684
Biso mean--39.5 46.84 -
Num. residues----438
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2547-2.37360.34341490.2632847299699
2.3736-2.52230.26831380.235828472985100
2.5223-2.7170.30211230.22328542977100
2.717-2.99040.25171500.213928523002100
2.9904-3.42310.25741300.190728692999100
3.4231-4.31230.1921390.154428663005100
4.3123-49.64810.17521410.144828452986100

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