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- PDB-8q5g: Crystal structure of nitroreductase from Bacillus tequilensis wit... -

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Basic information

Entry
Database: PDB / ID: 8q5g
TitleCrystal structure of nitroreductase from Bacillus tequilensis with covalent FMN
ComponentsNAD(P)H-dependent oxidoreductase
KeywordsOXIDOREDUCTASE / covalent flavinylation
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: 2 Å
AuthorsRozeboom, H.J. / Fraaije, M.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Fixing Flavins: Hijacking a Flavin Transferase for Equipping Flavoproteins with a Covalent Flavin Cofactor.
Authors: Tong, Y. / Kaya, S.G. / Russo, S. / Rozeboom, H.J. / Wijma, H.J. / Fraaije, M.W.
History
DepositionAug 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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)51,5384
Polymers50,6252
Non-polymers9132
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-27 kcal/mol
Surface area16900 Å2
Unit cell
Length a, b, c (Å)48.552, 62.638, 135.758
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 25312.668 Da / Num. of mol.: 2 / Mutation: A11D Y12G N13L F14S R15G H16A A17T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus tequilensis (bacteria) / Gene: G4P54_04090 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A6H0WK49
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 25% PEG1500 and PCB buffer pH 6-8 / PH range: 6-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2→48.55 Å / Num. obs: 28377 / % possible obs: 98.5 % / Redundancy: 6.1 % / CC1/2: 0.885 / Rmerge(I) obs: 0.226 / Rpim(I) all: 0.107 / Rrim(I) all: 0.252 / Χ2: 1.1 / Net I/σ(I): 13.7 / Num. measured all: 173576
Reflection shellResolution: 2→2.05 Å / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 1.482 / Num. measured all: 13430 / Num. unique obs: 2089 / CC1/2: 0.72 / Rpim(I) all: 0.648 / Rrim(I) all: 1.622 / Χ2: 1.08 / Net I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→46.08 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.905 / SU B: 6.261 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23388 1336 4.7 %RANDOM
Rwork0.19321 ---
obs0.19521 26818 97.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.156 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0 Å2-0 Å2
2---1.64 Å20 Å2
3---1.97 Å2
Refinement stepCycle: 1 / Resolution: 2→46.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3343 0 60 154 3557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123487
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163247
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.6514719
X-RAY DIFFRACTIONr_angle_other_deg0.5291.5767497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9555409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.408522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.91110612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0740.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024023
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02801
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_it2.2492.3341642
X-RAY DIFFRACTIONr_mcbond_other2.2492.3341642
X-RAY DIFFRACTIONr_mcangle_it3.2564.1782049
X-RAY DIFFRACTIONr_mcangle_other3.2554.1782050
X-RAY DIFFRACTIONr_scbond_it3.4522.7941845
X-RAY DIFFRACTIONr_scbond_other3.4212.791843
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4484.9182671
X-RAY DIFFRACTIONr_long_range_B_refined6.44124.034181
X-RAY DIFFRACTIONr_long_range_B_other6.42723.754159
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 95 -
Rwork0.299 1984 -
obs--99.66 %

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