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Yorodumi- PDB-5na4: NADH:quinone oxidoreductase (NDH-II) from Staphylococcus aureus -... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5na4 | |||||||||||||||||||||
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Title | NADH:quinone oxidoreductase (NDH-II) from Staphylococcus aureus - E172S mutant | |||||||||||||||||||||
Components | NADH dehydrogenase-like protein SAOUHSC_00878 | |||||||||||||||||||||
Keywords | OXIDOREDUCTASE / NADH / respiratory chain / energetic metabolism | |||||||||||||||||||||
Function / homology | Function and homology information NADH:quinone reductase (non-electrogenic) / NADH:ubiquinone reductase (non-electrogenic) activity / aerobic electron transport chain / NAD(P)H dehydrogenase (quinone) activity / plasma membrane Similarity search - Function | |||||||||||||||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | |||||||||||||||||||||
Authors | Brito, J.A. / Athayde, D. / Sousa, F.M. / Sena, F.V. / Pereira, M.M. / Archer, M. | |||||||||||||||||||||
Funding support | Portugal, 6items
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Citation | Journal: Biochim. Biophys. Acta / Year: 2017 Title: The key role of glutamate 172 in the mechanism of type II NADH:quinone oxidoreductase of Staphylococcus aureus. Authors: Sousa, F.M. / Sena, F.V. / Batista, A.P. / Athayde, D. / Brito, J.A. / Archer, M. / Oliveira, A.S.F. / Soares, C.M. / Catarino, T. / Pereira, M.M. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5na4.cif.gz | 173 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5na4.ent.gz | 134.9 KB | Display | PDB format |
PDBx/mmJSON format | 5na4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/5na4 ftp://data.pdbj.org/pub/pdb/validation_reports/na/5na4 | HTTPS FTP |
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-Related structure data
Related structure data | 5na1C 4xdb C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 44946.102 Da / Num. of mol.: 1 / Mutation: E172S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: SAOUHSC_00878 / Production host: Escherichia coli (E. coli) References: UniProt: Q2FZV7, Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors |
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#2: Chemical | ChemComp-FAD / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.67 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.2 M Sodium malonate dibasic monohydrate pH 7.0 Drop ratio - 1.6:1 (160 + 100 nL) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→67.65 Å / Num. obs: 19844 / % possible obs: 99.8 % / Redundancy: 7.7 % / Biso Wilson estimate: 71.81 Å2 / CC1/2: 1 / Rpim(I) all: 0.031 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.55→2.59 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 980 / CC1/2: 0.73 / Rpim(I) all: 0.352 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XDB 4xdb Resolution: 2.55→67.65 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.317 / SU Rfree Blow DPI: 0.228
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Displacement parameters | Biso mean: 58.34 Å2
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Refine analyze | Luzzati coordinate error obs: 0.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.55→67.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.69 Å / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: 9.7613 Å / Origin y: 11.2886 Å / Origin z: -24.2676 Å
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Refinement TLS group | Selection details: { A|* } |