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- PDB-8qyg: Crystal structure of Nitroreductase from Bacillus tequilensis -

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Basic information

Entry
Database: PDB / ID: 8qyg
TitleCrystal structure of Nitroreductase from Bacillus tequilensis
ComponentsNAD(P)H-dependent oxidoreductase
KeywordsOXIDOREDUCTASE / FMN-binding
Function / homology
Function and homology information


oxidoreductase activity, acting on other nitrogenous compounds as donors, with NAD or NADP as acceptor / 2,4,6-trinitrotoluene catabolic process / nucleotide binding / metal ion binding / cytosol
Similarity search - Function
Oxygen-insensitive NAD(P)H nitroreductase NfsB-like / : / Nitroreductase / Nitroreductase family / Nitroreductase-like
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / NAD(P)H-dependent oxidoreductase
Similarity search - Component
Biological speciesBacillus tequilensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsRozeboom, H.J. / Russo, S. / Fraaije, M.W. / Poelarends, G.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs J. / Year: 2024
Title: Biochemical, kinetic, and structural characterization of a Bacillus tequilensis nitroreductase.
Authors: Russo, S. / Rozeboom, H.J. / Wijma, H.J. / Poelarends, G.J. / Fraaije, M.W.
History
DepositionOct 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2024Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 23, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD(P)H-dependent oxidoreductase
B: NAD(P)H-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,35313
Polymers52,8042
Non-polymers1,54911
Water11,872659
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, and dynamic light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11040 Å2
ΔGint-65 kcal/mol
Surface area17890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.472, 84.279, 100.606
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NAD(P)H-dependent oxidoreductase


Mass: 26401.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus tequilensis (bacteria) / Gene: G4P54_04090 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6H0WK49

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Non-polymers , 5 types, 670 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 659 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium chloride, 20% PEG3350, MES buffer Ph 6.0
PH range: 5.9-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 1.15→46.5 Å / Num. obs: 157718 / % possible obs: 99.6 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.044 / Rrim(I) all: 0.088 / Χ2: 1.03 / Net I/σ(I): 10
Reflection shellResolution: 1.15→1.17 Å / % possible obs: 98.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.575 / Num. measured all: 26982 / Num. unique obs: 7745 / CC1/2: 0.76 / Rpim(I) all: 0.354 / Rrim(I) all: 0.679 / Χ2: 0.83 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→46.5 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.215 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14907 7880 5 %RANDOM
Rwork0.12304 ---
obs0.12431 149747 99.42 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.002 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å2-0 Å2-0 Å2
2---0.6 Å20 Å2
3---1.61 Å2
Refinement stepCycle: 1 / Resolution: 1.15→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3646 0 101 659 4406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0123976
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163681
X-RAY DIFFRACTIONr_angle_refined_deg1.8111.8385390
X-RAY DIFFRACTIONr_angle_other_deg0.6781.7878513
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6885473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.406524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.07710697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1090.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.024690
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02919
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it27.4440.9571859
X-RAY DIFFRACTIONr_mcbond_other27.4440.9571859
X-RAY DIFFRACTIONr_mcangle_it28.2581.7012343
X-RAY DIFFRACTIONr_mcangle_other28.2521.7012344
X-RAY DIFFRACTIONr_scbond_it5.7781.2142117
X-RAY DIFFRACTIONr_scbond_other5.7771.2142118
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other16.6282.1023048
X-RAY DIFFRACTIONr_long_range_B_refined17.08614.244991
X-RAY DIFFRACTIONr_long_range_B_other14.9211.334792
X-RAY DIFFRACTIONr_rigid_bond_restr5.21837657
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 582 -
Rwork0.207 10903 -
obs--98.91 %

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