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Yorodumi- PDB-6bdo: Structure of bacterial type II NADH dehydrogenase from Caldalkali... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bdo | ||||||
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Title | Structure of bacterial type II NADH dehydrogenase from Caldalkalibacillus thermarum complexed with a quinone inhibitor HQNO at 2.8A resolution | ||||||
Components | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE/INHIBITOR / ROSSMANN FOLD / NADH DEHYDROGENASE / OXIDOREDUCTASE / Flavo Protein / MEMBRANE PROTEIN / OXIDOREDUCTASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information aerobic electron transport chain / NAD(P)H dehydrogenase (quinone) activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Caldalkalibacillus thermarum TA2.A1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Cook, G.M. / Aragao, D. / Nakatani, Y. | ||||||
Funding support | New Zealand, 1items
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Citation | Journal: Biochim. Biophys. Acta / Year: 2018 Title: Structure of the NDH-2 - HQNO inhibited complex provides molecular insight into quinone-binding site inhibitors. Authors: Petri, J. / Shimaki, Y. / Jiao, W. / Bridges, H.R. / Russell, E.R. / Parker, E.J. / Aragao, D. / Cook, G.M. / Nakatani, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bdo.cif.gz | 308.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bdo.ent.gz | 246 KB | Display | PDB format |
PDBx/mmJSON format | 6bdo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bdo_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 6bdo_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 6bdo_validation.xml.gz | 57.6 KB | Display | |
Data in CIF | 6bdo_validation.cif.gz | 75.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/6bdo ftp://data.pdbj.org/pub/pdb/validation_reports/bd/6bdo | HTTPS FTP |
-Related structure data
Related structure data | 5wedS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 44571.988 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caldalkalibacillus thermarum TA2.A1 (bacteria) Gene: CathTA2_0279 / Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: F5L3B8 #2: Chemical | ChemComp-FAD / #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: 3.04 Å3/Da / Density % sol: 59.51 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M BICINE/TRIS BUFFER PH8.5 INCLUDING 10% (V/V) PEG 4000, 25% (V/V) ETHYLENE GLYCOL, 75 MM D,L-LYSINE, 1 MM 2-heptyl-4-hydroxyquinoline-N-oxide, 4% (V/V) dimethyl sulfoxide |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→43.345 Å / Num. obs: 52468 / % possible obs: 99.8 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.069 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.8→2.89 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.932 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 16726 / CC1/2: 0.446 / Rpim(I) all: 0.883 / Rsym value: 0.932 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WED Resolution: 2.8→43.345 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→43.345 Å
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Refine LS restraints |
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LS refinement shell |
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