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- PDB-7ple: ArsH of Paracoccus denitrificans -

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Basic information

Entry
Database: PDB / ID: 7ple
TitleArsH of Paracoccus denitrificans
ComponentsNADPH-dependent FMN reductase
KeywordsOXIDOREDUCTASE / ArsH / Flavinreductase / Paracoccus denitrificans
Function / homologyArsenate resistance ArsH / NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavoprotein-like superfamily / oxidoreductase activity / NADPH-dependent FMN reductase
Function and homology information
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKryl, M.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science Foundation16-18476S Czech Republic
CitationJournal: Antioxidants / Year: 2022
Title: The ArsH Protein Product of the Paracoccus denitrificans ars Operon Has an Activity of Organoarsenic Reductase and Is Regulated by a Redox-Responsive Repressor.
Authors: Sedlacek, V. / Kryl, M. / Kucera, I.
History
DepositionAug 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Refinement description / Category: citation / citation_author / refine
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _refine.pdbx_diffrn_id
Revision 1.2Jun 8, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3May 1, 2024Group: 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: NADPH-dependent FMN reductase
B: NADPH-dependent FMN reductase
C: NADPH-dependent FMN reductase
D: NADPH-dependent FMN reductase


Theoretical massNumber of molelcules
Total (without water)122,9724
Polymers122,9724
Non-polymers00
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14700 Å2
ΔGint-84 kcal/mol
Surface area32430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.950, 112.950, 204.410
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"

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Components

#1: Protein
NADPH-dependent FMN reductase


Mass: 30742.939 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (strain Pd 1222) (bacteria)
Strain: Pd 1222 / Gene: Pden_3133, Pden_3339 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A1B6S0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

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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: 3.06 Å3/Da / Density % sol: 59.82 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 4.77 M sodium acetate, 3% w/v 6-aminohexanoic acid, 80 mM HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
Reflection twinOperator: h,k,-l / Fraction: 0.12
ReflectionResolution: 2.6→97.82 Å / Num. obs: 47156 / % possible obs: 100 % / Redundancy: 2 % / Rpim(I) all: 0.108 / Net I/σ(I): 8.2
Reflection shellResolution: 2.6→2.69 Å / Num. unique obs: 4684 / CC1/2: 0.34 / Rpim(I) all: 0.226 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: custom homologous model

Resolution: 2.6→97.82 Å / Cross valid method: FREE R-VALUE / σ(F): 844.86 / Phase error: 39.439
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2775 2011 4.26 %
Rwork0.2553 45145 -
obs0.3151 47156 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.94 Å2
Refinement stepCycle: LAST / Resolution: 2.6→97.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6710 0 0 212 6922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00526836
X-RAY DIFFRACTIONf_angle_d0.80899221
X-RAY DIFFRACTIONf_chiral_restr0.04641048
X-RAY DIFFRACTIONf_plane_restr0.00541179
X-RAY DIFFRACTIONf_dihedral_angle_d16.18542524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.670.38191370.40133182X-RAY DIFFRACTION95.87
2.67-2.740.39851410.38533168X-RAY DIFFRACTION95.74
2.74-2.820.41781430.36713196X-RAY DIFFRACTION95.72
2.82-2.910.35971400.34933171X-RAY DIFFRACTION95.77
2.91-3.010.34761410.33883185X-RAY DIFFRACTION95.76
3.01-3.130.32641400.33323198X-RAY DIFFRACTION95.81
3.13-3.280.3551400.33523182X-RAY DIFFRACTION95.79
3.28-3.450.33491470.3253217X-RAY DIFFRACTION95.63
3.45-3.660.33461460.32023202X-RAY DIFFRACTION95.64
3.66-3.950.32141430.30793215X-RAY DIFFRACTION95.74
3.95-4.340.31381440.28153270X-RAY DIFFRACTION95.78
4.35-4.970.29071450.27063243X-RAY DIFFRACTION95.72
4.97-6.260.30041450.27223281X-RAY DIFFRACTION95.77
6.27-97.820.32731590.2983435X-RAY DIFFRACTION95.58

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