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Open data
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Basic information
Entry | Database: PDB / ID: 1ie3 | |||||||||
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Title | CRYSTAL STRUCTURE OF R153C E. COLI MALATE DEHYDROGENASE | |||||||||
![]() | MALATE DEHYDROGENASE | |||||||||
![]() | OXIDOREDUCTASE / dehydrogenase / malate dehydrogenase / substrate specificity | |||||||||
Function / homology | ![]() malate dehydrogenase activity / fermentation / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / anaerobic respiration / extrinsic component of membrane / tricarboxylic acid cycle / glycolytic process / oxidoreductase activity ...malate dehydrogenase activity / fermentation / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / anaerobic respiration / extrinsic component of membrane / tricarboxylic acid cycle / glycolytic process / oxidoreductase activity / protein homodimerization activity / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Bell, J.K. / Yennawar, H.P. / Wright, S.K. / Thompson, J.R. / Viola, R.E. / Banaszak, L.J. | |||||||||
![]() | ![]() Title: Structural Analyses of a Malate Dehydrogenase with a Variable Active Site Authors: Bell, J.K. / Yennawar, H.P. / Wright, S.K. / Thompson, J.R. / Viola, R.E. / Banaszak, L.J. #1: ![]() Title: Alteration of the Specificity of Malate Dehydrogenase by Chemical Modification of an Acitve Site Arginine Authors: Kirk, S.K. / Viola, R.E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 238.3 KB | Display | ![]() |
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PDB format | ![]() | 194.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32313.141 Da / Num. of mol.: 4 / Mutation: R153C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-PYR / | #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: 50.91 % | ||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: NaCacodylate, PEG 4000, Ammonium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 24 K / Details: used microseeding | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 297 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 15, 1999 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40 Å / Num. all: 95846 / Num. obs: 66535 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.4 % / Biso Wilson estimate: 44.9 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.361 / % possible all: 91.7 |
Reflection | *PLUS Lowest resolution: 40 Å / % possible obs: 87.5 % / Num. measured all: 95846 |
Reflection shell | *PLUS % possible obs: 90 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49 Å2 / ksol: 0.302 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→39.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.1 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 44.9 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.252 / % reflection Rfree: 9.7 % / Rfactor Rwork: 0.186 |