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Yorodumi- PDB-5kmq: The structure of I379E variant of type II NADH dehydrogenase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kmq | ||||||
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Title | The structure of I379E variant of type II NADH dehydrogenase from Caldalkalibacillus thermarum | ||||||
Components | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / ROSSMANN FOLD / NADH DEHYDROGENASE / I379E mutation | ||||||
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: 2.7 Å | ||||||
Authors | Cook, G.M. / Aragao, D. / Nakatani, Y. | ||||||
Funding support | New Zealand, 1items
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Citation | Journal: Sci Rep / Year: 2017 Title: The mechanism of catalysis by type-II NADH:quinone oxidoreductases. Authors: Blaza, J.N. / Bridges, H.R. / Aragao, D. / Dunn, E.A. / Heikal, A. / Cook, G.M. / Nakatani, Y. / Hirst, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kmq.cif.gz | 298 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kmq.ent.gz | 234.5 KB | Display | PDB format |
PDBx/mmJSON format | 5kmq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kmq_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 5kmq_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5kmq_validation.xml.gz | 55.6 KB | Display | |
Data in CIF | 5kmq_validation.cif.gz | 74 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/5kmq ftp://data.pdbj.org/pub/pdb/validation_reports/km/5kmq | HTTPS FTP |
-Related structure data
Related structure data | 5kmpC 5kmrC 5kmsC 4nwzS S: Starting model for refinement C: citing same article (ref.) |
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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: 44587.945 Da / Num. of mol.: 4 / Mutation: I379E 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: 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: 3.01 Å3/Da / Density % sol: 59.15 % |
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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 and 55mM D, L-lysine |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2015 |
Radiation | Monochromator: SILICON DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→47.6 Å / Num. obs: 56903 / % possible obs: 97.4 % / Redundancy: 3 % / Biso Wilson estimate: 52.8 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.7→2.77 Å / Redundancy: 3 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 1.6 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NWZ Resolution: 2.7→44.859 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→44.859 Å
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Refine LS restraints |
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LS refinement shell |
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