+Open data
-Basic information
Entry | Database: PDB / ID: 5f4b | |||||||||
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Title | Structure of B. abortus WrbA-related protein A (WrpA) | |||||||||
Components | NAD(P)H dehydrogenase (quinone) | |||||||||
Keywords | OXIDOREDUCTASE / Brucella / WrbA / NADH:quinone oxidoreductase / tetramer / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG | |||||||||
Function / homology | Function and homology information NAD(P)H dehydrogenase (quinone) / NADPH dehydrogenase (quinone) activity / NADH:ubiquinone reductase (non-electrogenic) activity / NAD binding / FMN binding / flavin adenine dinucleotide binding / NADP binding Similarity search - Function | |||||||||
Biological species | Brucella abortus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.498 Å | |||||||||
Authors | Herrou, J. / Czyz, D. / Willett, J.W. / Kim, H.S. / Chhor, G. / Endres, M. / Babnigg, G. / Kim, Y. / Joachimiak, A. / Crosson, S. / Midwest Center for Structural Genomics (MCSG) | |||||||||
Funding support | United States, 2items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f4b.cif.gz | 82 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f4b.ent.gz | 60.8 KB | Display | PDB format |
PDBx/mmJSON format | 5f4b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f4b_validation.pdf.gz | 1013.2 KB | Display | wwPDB validaton report |
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Full document | 5f4b_full_validation.pdf.gz | 1016.1 KB | Display | |
Data in XML | 5f4b_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 5f4b_validation.cif.gz | 19.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/5f4b ftp://data.pdbj.org/pub/pdb/validation_reports/f4/5f4b | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21737.699 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella abortus (strain 2308) (bacteria) Strain: 2308 / Gene: BAB1_1070 / Plasmid: pMCSG68 Details (production host): N-terminal 6 His tag cleavable by TEV protease Production host: Escherichia coli (E. coli) / Strain (production host): BL21 gold References: UniProt: Q2YQ23, NAD(P)H dehydrogenase (quinone) #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.87 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: 0.2 M potassium formate pH 7.3, 20 % (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 24, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 |
Reflection | Resolution: 2.498→44.7 Å / Num. all: 14207 / Num. obs: 14207 / % possible obs: 99.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 36.36 Å2 / Rsym value: 0.122 / Net I/σ(I): 11.26 |
Reflection shell | Resolution: 2.498→2.54 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 1.82 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: The 2.4 A structure of Apo-protein solved by SAD phasing Resolution: 2.498→44.696 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.54 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.498→44.696 Å
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Refine LS restraints |
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LS refinement shell |
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