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Yorodumi- PDB-1lpf: THREE-DIMENSIONAL STRUCTURE OF LIPOAMIDE DEHYDROGENASE FROM PSEUD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lpf | ||||||
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Title | THREE-DIMENSIONAL STRUCTURE OF LIPOAMIDE DEHYDROGENASE FROM PSEUDOMONAS FLUORESCENS AT 2.8 ANGSTROMS RESOLUTION. ANALYSIS OF REDOX AND THERMOSTABILITY PROPERTIES | ||||||
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 fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | ||||||
Authors | Mattevi, A. / Hol, W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1993 Title: Three-dimensional structure of lipoamide dehydrogenase from Pseudomonas fluorescens at 2.8 A resolution. Analysis of redox and thermostability properties. Authors: Mattevi, A. / Obmolova, G. / Kalk, K.H. / van Berkel, W.J. / 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: J.Gen.Microbiol. / Year: 1989 Title: Molecular Cloning and Sequence Determination of the Gene Encoding Lipoamide Dehydrogenase from Pseudomonas Fluorescens Authors: Benen, J.A.E. / Van Berkel, W.J.H. / Van Dongen, W.M.A.M. / Muller, F. / Dekok, A. #3: 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. | ||||||
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 GIVES ITS SEQUENTIAL NUMBER. THE DIGITS ARE SEPARATED BY THE CHAIN IDENTIFIER. BECAUSE THE HELIX IDENTIFIERS ARE RESTRICTED TO THREE CHARACTERS, HELIX 4-10 AND 4-11 OF BOTH CHAINS ARE LABELED 4A1, 4AA, 4B1 AND 4BA. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lpf.cif.gz | 182.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lpf.ent.gz | 145.2 KB | Display | PDB format |
PDBx/mmJSON format | 1lpf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/1lpf ftp://data.pdbj.org/pub/pdb/validation_reports/lp/1lpf | 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 360 AND PRO 451 IN BOTH CHAINS ARE CIS PROLINES. | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.192992, -0.39284, -0.899128), Vector: Details | THE TWO INDEPENDENTLY REFINED SUBUNITS ARE RELATED BY THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW. THIS TRANSFORMATION WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. AFTER SUPERPOSITION, THE RMS DIFFERENCE BETWEEN THE POSITIONS OF 3490 EQUIVALENT ATOMS IS 0.14 ANGSTROMS. | |
-Components
#1: Protein | Mass: 50082.527 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / References: UniProt: P14218, dihydrolipoyl dehydrogenase #2: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.7 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
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: 2.8 Å / Lowest resolution: 100 Å / Num. obs: 23546 / % possible obs: 78.2 % / Num. measured all: 40000 / Rmerge(I) obs: 0.0435 |
Reflection shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 40.7 % |
-Processing
Software |
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Refinement | Resolution: 2.8→10 Å / σ(F): 0 Details: DURING REFINEMENT, RESIDUES 42, 163, 387, AND 388 OF EACH CHAIN WERE IDENTIFIED AS THR. THEY ARE, IN FACT, VAL, SER, ALA, AND ALA, RESPECTIVELY. FOR THESE RESIDUES, IN THIS ENTRY, THE SIDE ...Details: DURING REFINEMENT, RESIDUES 42, 163, 387, AND 388 OF EACH CHAIN WERE IDENTIFIED AS THR. THEY ARE, IN FACT, VAL, SER, ALA, AND ALA, RESPECTIVELY. FOR THESE RESIDUES, IN THIS ENTRY, THE SIDE CHAIN ATOMS BEYOND CB HAVE BEEN REMOVED AND THE RESIDUES ARE PRESENTED WITH THEIR CORRECT RESIDUE NAMES. THIS MATTER IS BEING INVESTIGATED BY THE DEPOSITORS.
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Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 10 Å / Num. reflection all: 23164 / σ(F): 0 / Rfactor all: 0.192 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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