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Yorodumi- PDB-1lvl: THE REFINED STRUCTURE OF PSEUDOMONAS PUTIDA LIPOAMIDE DEHYDROGENA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lvl | ||||||
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Title | THE REFINED STRUCTURE OF PSEUDOMONAS PUTIDA LIPOAMIDE DEHYDROGENASE COMPLEXED WITH NAD+ AT 2.45 ANGSTROMS RESOLUTION | ||||||
Components | DIHYDROLIPOAMIDE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / cell redox homeostasis / glycolytic process / flavin adenine dinucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.45 Å | ||||||
Authors | Mattevi, A. / Hol, W.G.J. | ||||||
Citation | Journal: Proteins / Year: 1992 Title: The refined crystal structure of Pseudomonas putida lipoamide dehydrogenase complexed with NAD+ at 2.45 A resolution. Authors: Mattevi, A. / Obmolova, G. / Sokatch, J.R. / Betzel, C. / Hol, W.G. #1: Journal: J.Mol.Biol. / Year: 1991 Title: The Refined Crystal Structure of Lipoamide Dehydrogenase from Azotobacter Vinelandii at 2.2 Angstroms Resolution. A Comparison with the Structure of Glutathione Reductase Authors: Mattevi, A. / Schierbeek, A.J. / Hol, W.G.J. #2: Journal: Eur.J.Biochem. / Year: 1989 Title: Sequence Analysis of the Lpdv Gene for Lipoamide Dehydrogenase of Branched-Chain-Oxoacid Dehydrogenase of Pseudomonas Putida Authors: Burns, G. / Brown, T. / Hatter, K. / Sokatch, J.R. | ||||||
History |
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Remark 650 | HELIX EACH HELIX IS LABELED BY TWO DIGITS. THE FIRST INDICATES THE DOMAIN WHERE THE HELIX IS ...HELIX EACH HELIX IS LABELED BY TWO DIGITS. THE FIRST INDICATES THE DOMAIN WHERE THE HELIX IS LOCATED AND THE SECOND ONE GIVES ITS SEQUENTIAL NUMBER. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lvl.cif.gz | 100 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lvl.ent.gz | 81.1 KB | Display | PDB format |
PDBx/mmJSON format | 1lvl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/1lvl ftp://data.pdbj.org/pub/pdb/validation_reports/lv/1lvl | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: RESIDUES PRO 347 AND PRO 438 ARE CIS PROLINES. | ||||||||
Details | THE CRYSTALS CONTAIN ONE MONOMER PER ASYMMETRIC UNIT. THE SECOND SUBUNIT OF THE DIMER IS GENERATED BY THE TWOFOLD ROTATION ABOUT THE A AXIS: 1.00 0.00 0.00 0.00 0.00 -1.00 0.00 -108.118 0.00 0.00 -1.00 -151.077 |
-Components
#1: Protein | Mass: 48081.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / References: UniProt: P09063, dihydrolipoyl dehydrogenase |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-NAD / |
#4: Water | ChemComp-HOH / |
Compound details | PSEUDOMONAS PUTIDA IS THE ONLY KNOWN ORGANISM WHICH PRODUCES THREE DIFFERENT LIPOAMIDE ...PSEUDOMONA |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.95 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.45 Å / Lowest resolution: 12 Å / Num. obs: 18731 / Rmerge(I) obs: 0.072 |
Reflection shell | *PLUS Highest resolution: 2.45 Å / Lowest resolution: 2.5 Å / Rmerge(I) obs: 0.189 |
-Processing
Software |
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Refinement | Resolution: 2.45→10 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 2.45→10 Å
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Refinement | *PLUS Highest resolution: 2.45 Å / Lowest resolution: 10 Å / Num. reflection all: 18085 / σ(I): 0 / Rfactor all: 0.215 | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 47 Å2 | ||||||||||||||||||
Refine LS restraints | *PLUS
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