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- PDB-5f51: Structure of B. abortus WrbA-related protein A (apo) -

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Basic information

Entry
Database: PDB / ID: 5f51
TitleStructure of B. abortus WrbA-related protein A (apo)
ComponentsNAD(P)H dehydrogenase (quinone)
KeywordsOXIDOREDUCTASE / Brucella abortus / WrbA / NADH:quinone / WrpA
Function / homology
Function and homology information


NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / NADH:ubiquinone reductase (non-electrogenic) activity / NAD binding / FMN binding / NADP binding / flavin adenine dinucleotide binding
Similarity search - Function
NAD(P)H dehydrogenase (quinone), prokaryotic / Flavoprotein WrbA-like / NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavodoxin domain / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NAD(P)H dehydrogenase (quinone)
Similarity search - Component
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsHerrou, J. / Czyz, D. / Willett, J.W. / Kim, H.S. / Kim, Y. / Crosson, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI107792 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI107159 United States
CitationJournal: J.Bacteriol. / Year: 2016
Title: WrpA Is an Atypical Flavodoxin Family Protein under Regulatory Control of the Brucella abortus General Stress Response System.
Authors: Herrou, J. / Czyz, D.M. / Willett, J.W. / Kim, H.S. / Chhor, G. / Babnigg, G. / Kim, Y. / Crosson, S.
History
DepositionDec 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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: NAD(P)H dehydrogenase (quinone)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7332
Polymers23,6371
Non-polymers961
Water362
1
A: NAD(P)H dehydrogenase (quinone)
hetero molecules

A: NAD(P)H dehydrogenase (quinone)
hetero molecules

A: NAD(P)H dehydrogenase (quinone)
hetero molecules

A: NAD(P)H dehydrogenase (quinone)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9328
Polymers94,5474
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_554y,x,-z-1/21
crystal symmetry operation8_664-y+1,-x+1,-z-1/21
Buried area9020 Å2
ΔGint-124 kcal/mol
Surface area26630 Å2
MethodPISA
2
A: NAD(P)H dehydrogenase (quinone)
hetero molecules

A: NAD(P)H dehydrogenase (quinone)
hetero molecules

A: NAD(P)H dehydrogenase (quinone)
hetero molecules

A: NAD(P)H dehydrogenase (quinone)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9328
Polymers94,5474
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
Buried area6780 Å2
ΔGint-113 kcal/mol
Surface area28870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.280, 61.280, 128.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222

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Components

#1: Protein NAD(P)H dehydrogenase (quinone) / Flavoprotein WrbA / NAD(P)H:quinone oxidoreductase / NQO


Mass: 23636.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (strain 2308) (bacteria)
Strain: 2308 / Gene: BAB1_1070 / Plasmid: pET28c / Details (production host): KanR
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q2YQ23, NAD(P)H dehydrogenase (quinone)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.55 Å3/Da / Density % sol: 51.74 % / Description: rectangular
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 100 mM Sodium Acetate pH4.6, 300 mM Ammonium Sulfate, 20% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 7, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.53→44.32 Å / Num. all: 110348 / Num. obs: 8704 / % possible obs: 99.7 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 23.54
Reflection shellResolution: 2.53→2.62 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 4.1 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data scaling
PHENIX1.9_1692phasing
PHENIX1.9_1692model building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B6I

3b6i


Resolution: 2.53→44.318 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.268 412 4.74 %Random selection
Rwork0.239 ---
obs0.2405 8687 99.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.53→44.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1229 0 5 2 1236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031251
X-RAY DIFFRACTIONf_angle_d0.7151690
X-RAY DIFFRACTIONf_dihedral_angle_d12.975454
X-RAY DIFFRACTIONf_chiral_restr0.027191
X-RAY DIFFRACTIONf_plane_restr0.002217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5303-2.89640.35291350.29582683X-RAY DIFFRACTION100
2.8964-3.64890.34311230.28752732X-RAY DIFFRACTION100
3.6489-44.32480.23331540.21262860X-RAY DIFFRACTION99

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