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Yorodumi- PDB-1ldn: STRUCTURE OF A TERNARY COMPLEX OF AN ALLOSTERIC LACTATE DEHYDROGE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ldn | ||||||
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Title | STRUCTURE OF A TERNARY COMPLEX OF AN ALLOSTERIC LACTATE DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILUS AT 2.5 ANGSTROMS RESOLUTION | ||||||
Components | L-LACTATE DEHYDROGENASELactate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE(CHOH(D)-NAD(A)) | ||||||
Function / homology | Function and homology information L-lactate dehydrogenase / L-lactate dehydrogenase activity / glycolytic process / NAD binding / cytoplasm Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Wigley, D.B. / Gamblin, S.J. / Turkenburg, J.P. / Dodson, E.J. / Piontek, K. / Muirhead, H. / Holbrook, J.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1992 Title: Structure of a ternary complex of an allosteric lactate dehydrogenase from Bacillus stearothermophilus at 2.5 A resolution. Authors: Wigley, D.B. / Gamblin, S.J. / Turkenburg, J.P. / Dodson, E.J. / Piontek, K. / Muirhead, H. / Holbrook, J.J. #1: Journal: J.Mol.Biol. / Year: 1988 Title: Crystallization of a Ternary Complex of Lactate Dehydrogenase from Bacillus Stearothermophilus Authors: Wigley, D.B. / Muirhead, H. / Gamblin, S.J. / Holbrook, J.J. #2: Journal: Gene / Year: 1986 Title: Cloning, Expression and Complete Nucleotide Sequence of the Bacillus Stearothermophilus L-Lactate Dehydrogenase Gene Authors: Barstow, D.A. / Clarke, A.R. / Chia, W.N. / Wigley, D.B. / Sharman, A.F. / Holbrook, J.J. / Atkinson, T. / Minton, N.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ldn.cif.gz | 508.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ldn.ent.gz | 418.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ldn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/1ldn ftp://data.pdbj.org/pub/pdb/validation_reports/ld/1ldn | 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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2 |
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Unit cell |
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Atom site foot note | 1: RESIDUE PRO 139 OF EACH CHAIN IS A CIS PROLINE. | ||||||||
Details | THE COORDINATES OF ALL EIGHT MOLECULES OF THE ASYMMETRIC UNIT ARE PROVIDED BELOW BECAUSE OF THE REAL DIFFERENCES BETWEEN THEM DUE TO CRYSTAL CONTACTS. |
-Components
#1: Protein | Mass: 34745.527 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) References: UniProt: P00344, L-lactate dehydrogenase #2: Sugar | ChemComp-FBP / #3: Chemical | ChemComp-OXM / #4: Chemical | ChemComp-NAD / #5: Water | ChemComp-HOH / | Compound details | THE ENZYME WAS COCRYSTALLIZED IN THE PRESENCE OF THE COENZYME NADH AND THE ACTIVATOR FBP. THE NADH ...THE ENZYME WAS COCRYSTALL | Nonpolymer details | BECAUSE OF THE STATISTICAL DISORDER, TWO FBP MOLECULES WITH OCCUPANCIES OF 0.5 MODELLED WITH TWO ...BECAUSE OF THE STATISTICA | Sequence details | THE RESIDUES IN THIS ENTRY ARE NUMBERED SEQUENTIALLY FROM 15 - 331. SEE C.ABAD-ZAPATERO,J.P. ...THE RESIDUES IN THIS ENTRY ARE NUMBERED SEQUENTIAL | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.42 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging dropDetails: taken from Wigley, B., et al. (1988). J. Mol. Biol., 204, 1041-1044. | ||||||||||||||||||||||||
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: 2.5 Å / Lowest resolution: 30 Å / Num. obs: 62506 / Num. measured all: 99326 / Rmerge(I) obs: 0.097 |
-Processing
Software |
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Refinement | Rfactor obs: 0.157 / Highest resolution: 2.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.5 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 10 Å / Rfactor obs: 0.157 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |