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- PDB-7t33: The structure of Haemophilus influenzae Rd KW20 nitroreductase co... -

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Basic information

Entry
Database: PDB / ID: 7t33
TitleThe structure of Haemophilus influenzae Rd KW20 nitroreductase complexed with nicotinic acid
ComponentsPutative NAD(P)H nitroreductase
KeywordsOXIDOREDUCTASE / Nitroreductase Haemophilus influenzae Nicotinic acid
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
FLAVIN MONONUCLEOTIDE / NICOTINIC ACID / Putative NAD(P)H nitroreductase
Similarity search - Component
Biological speciesHaemophilus influenzae Rd KW20 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 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

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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)54,8468
Polymers53,4952
Non-polymers1,3516
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11230 Å2
ΔGint-78 kcal/mol
Surface area17360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.084, 57.084, 121.459
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#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
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#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-NIO / NICOTINIC ACID


Mass: 123.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
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: 2.14 Å3/Da / Density % sol: 42.41 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M potassium sodium tartrate tetrahydrate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 2.0 M ammonium sulfate

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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: Jun 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.3→49.4476 Å / Num. obs: 19464 / % possible obs: 99.13 % / Redundancy: 9.4 % / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 19.15
Reflection shellResolution: 2.301→2.384 Å / Redundancy: 5.2 % / Num. unique obs: 1838 / CC1/2: 0.807 / CC star: 0.945 / % possible all: 92.5

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WT2

6wt2


Resolution: 2.301→49.4476 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 26.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2212 1020 5.24 %
Rwork0.1867 18442 -
obs0.1886 19462 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.51 Å2 / Biso mean: 55.1389 Å2 / Biso min: 30.35 Å2
Refinement stepCycle: final / Resolution: 2.301→49.4476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3516 0 90 40 3646
Biso mean--56.26 48.55 -
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 (%)
2.3014-2.42280.29961260.25242510263694
2.4228-2.57450.26141320.240326772809100
2.5745-2.77330.30011420.23826442786100
2.7733-3.05240.23121320.240326792811100
3.0524-3.49390.25262080.209125972805100
3.4939-4.40160.2331070.16727202827100
4.4016-49.44760.1711730.148526152788100

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