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Yorodumi- PDB-3lad: REFINED CRYSTAL STRUCTURE OF LIPOAMIDE DEHYDROGENASE FROM AZOTOBA... -
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-Basic information
Entry | Database: PDB / ID: 3lad | ||||||
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Title | REFINED CRYSTAL STRUCTURE OF LIPOAMIDE DEHYDROGENASE FROM AZOTOBACTER VINELANDII AT 2.2 ANGSTROMS RESOLUTION. A COMPARISON WITH THE STRUCTURE OF GLUTATHIONE REDUCTASE | ||||||
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 | Azotobacter vinelandii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Mattevi, A. / Schierbeek, A.J. / Hol, W.G.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1991 Title: Refined crystal structure of lipoamide dehydrogenase from Azotobacter vinelandii at 2.2 A resolution. A comparison with the structure of glutathione reductase. Authors: Mattevi, A. / Schierbeek, A.J. / Hol, W.G. #1: Journal: J.Mol.Biol. / Year: 1989 Title: X-Ray Structure of Lipoamide Dehydrogenase from Azotobacter Vinelandii Determined by a Combination of Molecular and Isomorphous Replacement Techniques Authors: Schierbeek, A.J. / Swarte, M.B.A. / Dijkstra, B.W. / Vriend, G. / Read, R.J. / Hol, W.G.J. / Drenth, J. / Betzel, C. #2: Journal: Eur.J.Biochem. / Year: 1988 Title: Lipoamide Dehydrogenase from Azotobacter Vinelandii: Molecular Cloning, Organization and Sequence Analysis of the Gene Authors: Westphal, A.H. / Dekok, A. #3: Journal: J.Mol.Biol. / Year: 1983 Title: Crystallization and Preliminary X-Ray Investigation of Lipoamide Dehydrogenase from Azotobacter Vinelandii Authors: Schierbeek, A.J. / Van Derlaan, J.M. / Groendijk, H. / Wierenga, R.K. / Drenth, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lad.cif.gz | 193 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lad.ent.gz | 152.4 KB | Display | PDB format |
PDBx/mmJSON format | 3lad.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/3lad ftp://data.pdbj.org/pub/pdb/validation_reports/la/3lad | 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: HIS A 359 - PRO A 360 OMEGA =122.43 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: CIS PROLINE - PRO A 451 3: HIS B 359 - PRO B 360 OMEGA =324.57 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 4: CIS PROLINE - PRO B 451 | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.083696, 0.801095, 0.592657), Vector: Details | THE TRANSFORMATION PROVIDED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*. AFTER SUPERPOSITION, THE RMS DIFFERENCE BETWEEN THE POSITIONS OF 472 EQUIVALENT CARBON ALPHA ATOMS IS 0.63 ANGSTROMS. | |
-Components
#1: Protein | Mass: 49494.750 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azotobacter vinelandii (bacteria) / References: UniProt: P18925, dihydrolipoyl dehydrogenase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.81 % | |||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
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-Processing
Software |
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Refinement | Highest resolution: 2.2 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Highest resolution: 2.2 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 8 Å / Num. reflection obs: 44294 / σ(F): 2 / Rfactor obs: 0.192 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |