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- PDB-7cza: Hexachlorobenzene monooxygenase (HcbA1) from Nocardioides sp. str... -

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Basic information

Entry
Database: PDB / ID: 7cza
TitleHexachlorobenzene monooxygenase (HcbA1) from Nocardioides sp. strain PD653 complexed with FMN
ComponentsHexachlorobenzene oxidative dehalogenase
KeywordsOXIDOREDUCTASE / hexachlorobenzene / dehalogenase / monooxygenase / FMN
Function / homologyNitrilotriacetate monooxygenase component A/pristinamycin IIA synthase subunit A / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / FLAVIN MONONUCLEOTIDE / Hexachlorobenzene oxidative dehalogenase
Function and homology information
Biological speciesNocardioides sp. PD653 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsGuo, Y. / Zheng, J.T. / Zhou, N.Y.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0901200 China
National Natural Science Foundation of China (NSFC)31570056,31770068 China
CitationJournal: Appl.Environ.Microbiol. / Year: 2020
Title: Hexachlorobenzene Monooxygenase Substrate Selectivity and Catalysis: Structural and Biochemical Insights.
Authors: Guo, Y. / Li, D.F. / Ji, H. / Zheng, J. / Zhou, N.Y.
History
DepositionSep 7, 2020Deposition site: PDBJ / Processing site: PDBJ
SupersessionSep 16, 2020ID: 6LR5
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: 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 / _citation_author.name
Revision 1.2Feb 10, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hexachlorobenzene oxidative dehalogenase
B: Hexachlorobenzene oxidative dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,2974
Polymers100,3852
Non-polymers9132
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-46 kcal/mol
Surface area29460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.347, 139.843, 171.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Hexachlorobenzene oxidative dehalogenase


Mass: 50192.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardioides sp. PD653 (bacteria) / Gene: hcbA1, PD653_2189 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): BL21(DE3)-groELS / References: UniProt: A0A1V1W347
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
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: 3.35 Å3/Da / Density % sol: 63.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 0.1 M Bis-Tris (pH 5.5) and 1.8 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 110 K / Ambient temp details: liquid Nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.77 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 22164 / % possible obs: 99.8 % / Redundancy: 6.6 % / CC1/2: 0.817 / Net I/σ(I): 4.95
Reflection shellResolution: 3.2→3.26 Å / Num. unique obs: 1063 / CC1/2: 0.817

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B9N

3b9n


Resolution: 3.21→47.79 Å / Cross valid method: THROUGHOUT
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.29734 1099 -
Rwork0.24342 --
obs-20990 98.97 %
Displacement parametersBiso mean: 37.46 Å2
Refinement stepCycle: LAST / Resolution: 3.21→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6596 0 62 0 6658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01276820
X-RAY DIFFRACTIONf_angle_d1.63669252
X-RAY DIFFRACTIONf_chiral_restr0.0865982
X-RAY DIFFRACTIONf_plane_restr0.00861208
X-RAY DIFFRACTIONf_dihedral_angle_d30.04672468
LS refinement shellResolution: 3.213→3.297 Å
RfactorNum. reflection% reflection
Rfree0.41 --
Rwork0.327 1361 -
obs--88.91 %

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