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Yorodumi- PDB-2ldx: CHARACTERIZATION OF THE ANTIGENIC SITES ON THE REFINED 3-ANGSTROM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ldx | ||||||||||||
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Title | CHARACTERIZATION OF THE ANTIGENIC SITES ON THE REFINED 3-ANGSTROMS RESOLUTION STRUCTURE OF MOUSE TESTICULAR LACTATE DEHYDROGENASE C4 | ||||||||||||
Components | APO-LACTATE DEHYDROGENASE | ||||||||||||
Keywords | OXIDOREDUCTASE(CHOH(D)-NAD(A)) | ||||||||||||
Function / homology | Function and homology information lactate biosynthetic process from pyruvate / Pyruvate metabolism / lactate oxidation / flagellated sperm motility / ATP biosynthetic process / L-lactate dehydrogenase / L-lactate dehydrogenase activity / motile cilium / pyruvate metabolic process / cilium ...lactate biosynthetic process from pyruvate / Pyruvate metabolism / lactate oxidation / flagellated sperm motility / ATP biosynthetic process / L-lactate dehydrogenase / L-lactate dehydrogenase activity / motile cilium / pyruvate metabolic process / cilium / carbohydrate metabolic process / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.96 Å | ||||||||||||
Authors | Griffith, J.P. / Rossmann, M.G. | ||||||||||||
Citation | Journal: J.Biol.Chem. / Year: 1987 Title: Characterization of the antigenic sites on the refined 3-A resolution structure of mouse testicular lactate dehydrogenase C4. Authors: Hogrefe, H.H. / Griffith, J.P. / Rossmann, M.G. / Goldberg, E. #1: Journal: J.Biol.Chem. / Year: 1979 Title: The Structure of Mouse Testicular Lactate Dehydrogenase Isoenzyme C4 at 2.9 Angstroms Resolution Authors: Musick, W.D.L. / Rossmann, M.G. #2: Journal: J.Mol.Biol. / Year: 1976 Title: A Low-Resolution Study of Testicular Lactate Dehydrogenase Using the Molecular Replacement Technique Authors: Musick, W.D.L. / Adams, A.D. / Rossmann, M.G. / Wheat, T.E. / Goldberg, E. #3: Journal: J.Mol.Biol. / Year: 1973 Title: A Crystalline Form of Testes-Specific Lactate Dehydrogenase Authors: Adams, A.D. / Adams, M.J. / Rossmann, M.G. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ldx.cif.gz | 251.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ldx.ent.gz | 197.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ldx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ldx_validation.pdf.gz | 452.5 KB | Display | wwPDB validaton report |
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Full document | 2ldx_full_validation.pdf.gz | 675.7 KB | Display | |
Data in XML | 2ldx_validation.xml.gz | 80.7 KB | Display | |
Data in CIF | 2ldx_validation.cif.gz | 104 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/2ldx ftp://data.pdbj.org/pub/pdb/validation_reports/ld/2ldx | HTTPS FTP |
-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: RESIDUE PRO 138 IS A CIS-PROLINE. | ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 35866.605 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P00342, L-lactate dehydrogenase #2: Water | ChemComp-HOH / | Compound details | THE SECONDARY STRUCTURE SPECIFICAT | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.51 % | |||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.4 / Method: microdialysis / Details: seeding | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.96 Å / Lowest resolution: 10 Å / % possible obs: 0.66 % / Num. measured all: 20475 / Rmerge(I) obs: 0.254 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.96→10 Å / Rfactor obs: 0.256 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.96→10 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.96 Å / Lowest resolution: 10 Å / Rfactor obs: 0.256 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |