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Yorodumi- PDB-1mld: REFINED STRUCTURE OF MITOCHONDRIAL MALATE DEHYDROGENASE FROM PORC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mld | ||||||
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Title | REFINED STRUCTURE OF MITOCHONDRIAL MALATE DEHYDROGENASE FROM PORCINE HEART AND THE CONSENSUS STRUCTURE FOR DICARBOXYLIC ACID OXIDOREDUCTASES | ||||||
Components | MALATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE(NAD(A)-CHOH(D)) | ||||||
Function / homology | Function and homology information malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / tricarboxylic acid cycle / aerobic respiration / protein-folding chaperone binding / carbohydrate metabolic process / mitochondrial matrix / protein homodimerization activity / mitochondrion / cytoplasm Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.83 Å | ||||||
Authors | Gleason, W.B. / Fu, Z. / Birktoft, J.J. / Banaszak, L.J. | ||||||
Citation | Journal: Biochemistry / Year: 1994 Title: Refined crystal structure of mitochondrial malate dehydrogenase from porcine heart and the consensus structure for dicarboxylic acid oxidoreductases. Authors: Gleason, W.B. / Fu, Z. / Birktoft, J. / Banaszak, L. #1: Journal: Biochemistry / Year: 1993 Title: Determinants of Protein Thermostability Observed in the 1.9 Angstrom Crystal Structure of Malate Dehydrogenase from the Thermophilic Bacterium Thermus Flavus Authors: Kelly, C.A. / Nishiyama, M. / Ohnishi, Y. / Beppu, T. / Birktoft, J.J. #2: Journal: Biochemistry / Year: 1989 Title: Refined Crystal Structure of Cytoplasmic Malate Dehydrogenase at 2.5 Angstroms Resolution Authors: Birktoft, J.J. / Rhodes, G. / Banaszak, L.J. #3: Journal: Biochem.Soc.Trans. / Year: 1989 Title: Comparison of the Molecular Structures of Cytoplasmic and Mitochondrial Malate Dehydrogenases Authors: Birktoft, J.J. / Fu, Z. / Carnahan, G.E. / Rodes, G. / Roderick, S.L. / Banaszak, L.J. #4: Journal: J.Biol.Chem. / Year: 1986 Title: The Three Dimensional Structure of Porcine Heart Mitochondrial Malate Dehydrogenase at 3.0 Angstrom Resolution Authors: Roderick, S.L. / Banaszak, L.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mld.cif.gz | 242 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mld.ent.gz | 198.8 KB | Display | PDB format |
PDBx/mmJSON format | 1mld.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mld_validation.pdf.gz | 411.4 KB | Display | wwPDB validaton report |
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Full document | 1mld_full_validation.pdf.gz | 440.3 KB | Display | |
Data in XML | 1mld_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 1mld_validation.cif.gz | 44 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/1mld ftp://data.pdbj.org/pub/pdb/validation_reports/ml/1mld | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO A 119 / 2: CIS PROLINE - PRO A 190 / 3: CIS PROLINE - PRO B 119 / 4: CIS PROLINE - PRO B 190 / 5: CIS PROLINE - PRO C 119 / 6: CIS PROLINE - PRO C 190 / 7: CIS PROLINE - PRO D 119 / 8: CIS PROLINE - PRO D 190 |
-Components
#1: Protein | Mass: 33120.531 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P00346, malate dehydrogenase #2: Chemical | ChemComp-CIT / #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: 2.59 Å3/Da / Density % sol: 52.43 % | ||||||||||||
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Crystal grow | *PLUS pH: 5.8 / Method: unknownDetails: referred to 'Roderick, S.L.', (1986) J.Biol.Chem., 261, 9461-9464 | ||||||||||||
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: 1.83 Å / Num. obs: 91000 / Rmerge(I) obs: 0.145 |
-Processing
Software |
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Refinement | Resolution: 1.83→6 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 1.83→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.211 / Rfactor Rwork: 0.211 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.2 |