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- PDB-5u8u: Dihydrolipoamide dehydrogenase (LpdG) from Pseudomonas aeruginosa -
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Open data
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Basic information
Entry | Database: PDB / ID: 5u8u | ||||||
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Title | Dihydrolipoamide dehydrogenase (LpdG) from Pseudomonas aeruginosa | ||||||
![]() | Dihydrolipoyl dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / dihydrolipoamide dehydrogenase / NAD(H) binding | ||||||
Function / homology | ![]() dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / cell redox homeostasis / glycolytic process / flavin adenine dinucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Glasser, N.R. / Wang, B.X. / Hoy, J.A. / Newman, D.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The Pyruvate and alpha-Ketoglutarate Dehydrogenase Complexes of Pseudomonas aeruginosa Catalyze Pyocyanin and Phenazine-1-carboxylic Acid Reduction via the Subunit Dihydrolipoamide Dehydrogenase. Authors: Glasser, N.R. / Wang, B.X. / Hoy, J.A. / Newman, D.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 951 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5u8vC ![]() 5u8wC ![]() 1lpfS C: citing same article ( S: Starting model for refinement |
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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: 50510.023 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: UCBPP-PA14 / Gene: lpdG, PA14_43970 / Production host: ![]() ![]() References: UniProt: A0A0H2Z9F5, UniProt: Q9I3D1*PLUS, dihydrolipoyl dehydrogenase #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-DMS / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.07 % / Description: bricks or cubes |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.1 / Details: PEG 3350, HEPES, KCl, microseeding |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→38.76 Å / Num. obs: 443473 / % possible obs: 99.9 % / Redundancy: 13.6 % / CC1/2: 1 / Rmerge(I) obs: 0.062 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 13.4 % / Rmerge(I) obs: 1.736 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.659 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1LPF Resolution: 1.35→38.755 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.08 / Phase error: 15.74
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→38.755 Å
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Refine LS restraints |
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LS refinement shell |
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