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Yorodumi- PDB-1ldm: Refined crystal structure of dogfish M4 apo-lactate dehydrogenase -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ldm | ||||||
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Title | Refined crystal structure of dogfish M4 apo-lactate dehydrogenase | ||||||
Components | M4 LACTATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Squalus acanthias (spiny dogfish) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | ||||||
Authors | Griffith, J.P. / Rossmann, M.G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1987 Title: Refined crystal structure of dogfish M4 apo-lactate dehydrogenase. Authors: Abad-Zapatero, C. / Griffith, J.P. / Sussman, J.L. / Rossmann, M.G. #1: Journal: J.Mol.Biol. / Year: 1976 Title: A Comparison of the Structures of Apo Dogfish M4 Lactate Dehydrogenase and its Ternary Complexes Authors: White, J.L. / Hackert, M.L. / Buehner, M. / Adams, M.J. / Ford, G.C. / Lentzjunior, P.J. / Smiley, I.E. / Steindel, S.J. / Rossmann, M.G. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1977 Title: Structural Adaptations of Lactate Dehydrogenase Isozymes Authors: Eventoff, W. / Rossmann, M.G. / Taylor, S.S. / Torff, H.-J. / Meyer, H. / Keil, W. / Kiltz, H.-H. #3: Journal: J.Mol.Biol. / Year: 1975 Title: A 5 Angstroms X-Ray Diffraction Study of Coenzyme-Deficient Lactate Dehydrogenase,Nad-Pyruvate Ternary Complex Authors: White, J. / Rossmann, M.G. / Ford, G.C. #4: Journal: Isozymes-Molecular Structure / Year: 1975 Title: A Structural Comparison of Porcine B4 and Dogfish A4 Isozymes of Lactate Dehydrogenase Authors: Eventoff, W. / Hackert, M.L. / Steindel, S.J. / Rossmann, M.G. #5: Journal: The Enzymes,Third Edition / Year: 1975 Title: Lactate Dehydrogenase Authors: Holbrook, J.J. / Liljas, A. / Steindel, S.J. / Rossmann, M.G. #6: Journal: Annu.Rev.Biochem. / Year: 1974 Title: X-Ray Studies of Protein Interactions Authors: Liljas, A. / Rossmann, M.G. #7: Journal: Nature / Year: 1974 Title: Chemical and Biological Evolution of a Nucleotide Binding Protein Authors: Rossmann, M.G. / Moras, D. / Olsen, K.W. #8: Journal: J.Mol.Biol. / Year: 1974 Title: Recognition of Structural Domains in Globular Proteins Authors: Rossmann, M.G. / Liljas, A. #9: Journal: Biochem.Biophys.Res.Commun. / Year: 1973 Title: Atomic Co-Ordinates for Dogfish M4 Apo-Lactate Dehydrogenase Authors: Adams, M.J. / Ford, G.C. / Liljas, A. / Rossmann, M.G. #10: Journal: Proc.Natl.Acad.Sci.USA / Year: 1973 Title: Structure-Function Relationships in Lactate Dehydrogenase Authors: Adams, M.J. / Buehner, M. / Chandrasekhar, K. / Ford, G.C. / Hackert, M.L. / Liljas, A. / Rossmann, M.G. / Smiley, I.E. / Allison, W.S. / Everse, J. / Kaplan, N.O. / Taylor, S.S. #11: Journal: Proc.Natl.Acad.Sci.USA / Year: 1973 Title: Amino-Acid Sequence of Dogfish M4 Lactate Dehydrogenase Authors: Taylor, S.S. / Oxley, S.S. / Allison, W.S. / Kaplan, N.O. #12: Journal: J.Mol.Biol. / Year: 1973 Title: Molecular Symmetry Axes and Subunit Interfaces in Certain Dehydrogenases Authors: Rossmann, M.G. / Adams, M.J. / Buehner, M. / Ford, G.C. / Hackert, M.L. / Liljas, A. / Rao, S.T. / Banaszak, L.J. / Hill, E. / Tsernoglou, D. / Webb, L. #13: Journal: J.Mol.Biol. / Year: 1973 Title: Functional Anion Binding Sites in Dogfish M4 Lactate Dehydrogenase Authors: Adams, M.J. / Liljas, A. / Rossmann, M.G. #14: Journal: J.Mol.Biol. / Year: 1973 Title: Binding of Oxamate to the Apoenzyme of Dogfish M4 Lactate Dehydrogenase Authors: Mcphersonjunior, A. #15: Journal: J.Mol.Biol. / Year: 1973 Title: Conformation of Coenzyme Fragments When Bound to Lactate Dehydrogenase Authors: Chandrasekhar, K. / Mcphersonjunior, A. / Adams, M.J. / Rossmann, M.G. #16: Journal: J.Mol.Biol. / Year: 1971 Title: The 5 Angstroms Resolution Structure of an Abortive Ternary Complex of Lactate Dehydrogenase and its Comparison with the Apo-Enzyme Authors: Smiley, I.E. / Koekoek, R. / Adams, M.J. / Rossmann, M.G. #17: Journal: Nature / Year: 1970 Title: Structure of Lactate Dehydrogenase at 2.8 Angstroms Resolution Authors: Adams, M.J. / Ford, G.C. / Koekoek, R. / Lentzjunior, P.J. / Mcphersonjunior, A. / Rossmann, M.G. / Smiley, I.E. / Schevitz, R.W. / Wonacott, A.J. #18: Journal: J.Mol.Biol. / Year: 1969 Title: Low Resolution Study of Crystalline L-Lactate Dehydrogenase Authors: Adams, M.J. / Haas, D.J. / Jeffery, B.A. / Mcphersonjunior, A. / Mermall, H.L. / Rossmann, M.G. / Schevitz, R.W. / Wonacott, A.J. #19: Journal: Proc.Natl.Acad.Sci.USA / Year: 1967 Title: The Crystal Structure of Lactic Dehydrogenase Authors: Rossmann, M.G. / Jeffery, B.A. / Main, P. / Warren, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ldm.cif.gz | 99.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ldm.ent.gz | 62 KB | Display | PDB format |
PDBx/mmJSON format | 1ldm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ldm_validation.pdf.gz | 482.2 KB | Display | wwPDB validaton report |
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Full document | 1ldm_full_validation.pdf.gz | 609.2 KB | Display | |
Data in XML | 1ldm_validation.xml.gz | 33.4 KB | Display | |
Data in CIF | 1ldm_validation.cif.gz | 44.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/1ldm ftp://data.pdbj.org/pub/pdb/validation_reports/ld/1ldm | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Atom site foot note | 1: RESIDUE PRO 139 IS A CIS PROLINE. | ||||||||
Symmetry | Point symmetry: (Schoenflies symbol: D2 (2x2 fold dihedral)) | ||||||||
Details | NON-CRYSTALLOGRAPHIC SYMMETRY ELEMENTS CORRESPONDING TO THE THREE ORTHOGONAL MOLECULAR SYMMETRY AXES ARE PRESENTED ON THE *MTRIX* RECORDS BELOW. |
-Components
#1: Protein | Mass: 36327.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Squalus acanthias (spiny dogfish) / References: UniProt: P00341, L-lactate dehydrogenase | ||||
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#2: Chemical | ChemComp-NAD / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE RESIDUES IN THIS ENTRY ARE NUMBERED SEQUENTIALLY FROM 1 - 329. SEE THE PAPER CITED AS REFERENCE ...THE RESIDUES IN THIS ENTRY ARE NUMBERED SEQUENTIAL | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.98 % |
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Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: referred to 'Pesca, A. J.', (1967) J.Biol.Chem., 242, 2151-2167 |
Components of the solutions | *PLUS Conc.: 30 %sat / Common name: ammonium sulfate |
-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.1→6 Å / Rfactor obs: 0.173 Details: SPACE GROUP C 4 21 2 (WHICH, MORE PROPERLY, SHOULD BE NAMED C 4 2 21) IS A NON-STANDARD REPRESENTATION OF SPACE GROUP P 4 21 2. IN THIS CASE THE AXES OF THE UNIT CELL ARE CONSIDERED TO BE LEFT-HANDED. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→6 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 6 Å / σ(I): 2 / Rfactor obs: 0.173 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |