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- PDB-2cvq: Crystal structure of NAD(H)-dependent malate dehydrogenase comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2cvq | ||||||
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Title | Crystal structure of NAD(H)-dependent malate dehydrogenase complexed with NADPH | ||||||
![]() | Malate dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / NAD-dependent-MDH NADP+ complex | ||||||
Function / homology | ![]() malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / oxaloacetate metabolic process / NADH metabolic process / tricarboxylic acid cycle Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tomita, T. / Fushinobu, S. / Kuzuyama, T. / Nishiyama, M. | ||||||
![]() | ![]() Title: Crystal structure of NAD-dependent malate dehydrogenase complexed with NADP(H) Authors: Tomita, T. / Fushinobu, S. / Kuzuyama, T. / Nishiyama, M. #1: ![]() Title: Determinants of protein thermostability observed in the 1.9-A 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: J.Mol.Biol. / Year: 1991 Title: Preliminary X-ray diffraction analysis of a crystallizable mutant of malate dehydrogenase from the thermophile Thermus flavus Authors: Kelly, C.A. / Sarfaty, S. / Nishiyama, M. / Beppu, T. / Birktoft, J.J. #3: ![]() Title: Refined crystal structure of cytoplasmic malate dehydrogenase at 2.5-A resolution Authors: Birktoft, J.J. / Rhodes, G. / Banaszak, L.J. #4: Journal: J.Biol.Chem. / Year: 1986 Title: Nucleotide sequence of the malate dehydrogenase gene of Thermus flavus and its mutation directing an increase in enzyme activity Authors: Nishiyama, M. / Matsubara, N. / Yamamoto, K. / Iijima, S. / Uozumi, T. / Beppu, T. #5: Journal: J.Biol.Chem. / Year: 1983 Title: The presence of a histidine-aspartic acid pair in the active site of 2-hydroxyacid dehydrogenases. X-ray refinement of cytoplasmic malate dehydrogenase Authors: Birktoft, J.J. / Banaszak, L.J. #6: ![]() Title: Malate Dehydrogenases Authors: Banaszak, L.J. / Bradshaw, R.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144.6 KB | Display | ![]() |
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PDB format | ![]() | 113 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 30.9 KB | Display | |
Data in CIF | ![]() | 42.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The second part of the biological assembly is generated by the two fold axis: -z, -x+1, y. |
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Components
#1: Protein | Mass: 35466.785 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-TRS / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 6, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→69.07 Å / Num. all: 47323 / Num. obs: 43032 / % possible obs: 90.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 17.8 Å2 |
Reflection shell | Resolution: 2.08→2.21 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Malate Dehydrogenase Resolution: 2.08→40.06 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2209383.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.7126 Å2 / ksol: 0.377332 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.08→40.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.08→2.21 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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