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Yorodumi- PDB-5u8v: Dihydrolipoamide dehydrogenase (LpdG) from Pseudomonas aeruginosa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u8v | ||||||
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Title | Dihydrolipoamide dehydrogenase (LpdG) from Pseudomonas aeruginosa bound to NAD+ | ||||||
Components | Dihydrolipoyl dehydrogenaseDihydrolipoamide dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / dihydrolipoamide dehydrogenase / NAD(H) binding | ||||||
Function / homology | Function and homology information dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / flavin adenine dinucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Glasser, N.R. / Wang, B.X. / Hoy, J.A. / Newman, D.K. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u8v.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5u8v.ent.gz | 896.7 KB | Display | PDB format |
PDBx/mmJSON format | 5u8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/5u8v ftp://data.pdbj.org/pub/pdb/validation_reports/u8/5u8v | HTTPS FTP |
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-Related structure data
Related structure data | 5u8uC 5u8wC 1lpfS 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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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.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria) Strain: UCBPP-PA14 / Gene: lpdG, PA14_43970 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0H2Z9F5, dihydrolipoyl dehydrogenase #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-NAD / #4: Chemical | ChemComp-DMS / #5: 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: 2.58 Å3/Da / Density % sol: 52.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1 / Details: PEG 3350, HEPES, KCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 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: 1.45→38.901 Å / Num. obs: 361955 / % possible obs: 100 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 13 % / Rmerge(I) obs: 1.672 / Mean I/σ(I) obs: 1.5 / CC1/2: 0.608 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LPF Resolution: 1.45→38.901 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.21 / Phase error: 16.82
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→38.901 Å
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Refine LS restraints |
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LS refinement shell |
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