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- PDB-5kmq: The structure of I379E variant of type II NADH dehydrogenase from... -
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Open data
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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 | ||||||
![]() | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | ||||||
![]() | OXIDOREDUCTASE / ROSSMANN FOLD / NADH DEHYDROGENASE / I379E mutation | ||||||
Function / homology | ![]() aerobic electron transport chain / NAD(P)H dehydrogenase (quinone) activity / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cook, G.M. / Aragao, D. / Nakatani, Y. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 298 KB | Display | ![]() |
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PDB format | ![]() | 234.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 55.6 KB | Display | |
Data in CIF | ![]() | 74 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kmpC ![]() 5kmrC ![]() 5kmsC ![]() 4nwzS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() Gene: CathTA2_0279 / Plasmid: PTRC99A / Production host: ![]() ![]() #2: Chemical | ChemComp-FAD / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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