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- PDB-3fmx: Crystal structure of Tartrate dehydrogenase from Pseudomonas puti... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3fmx | ||||||
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Title | Crystal structure of Tartrate dehydrogenase from Pseudomonas putida complexed with NADH | ||||||
![]() | Tartrate dehydrogenase/decarboxylase | ||||||
![]() | OXIDOREDUCTASE / Lyase / Magnesium / Manganese / NAD | ||||||
Function / homology | ![]() D-malate dehydrogenase (decarboxylating) / tartrate dehydrogenase / tartrate decarboxylase / tartrate dehydrogenase activity / D-malate dehydrogenase (decarboxylating) (NAD+) activity / tartrate decarboxylase activity / NAD binding / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Malik, R. / Viola, R.E. | ||||||
![]() | ![]() Title: Structural Characterization of Tartrate Dehydrogenase: a versatile enzyme catalyzing multiple reactions Authors: Malik, R. / 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 | ![]() | 85.8 KB | Display | ![]() |
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PDB format | ![]() | 63.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3flkS S: Starting model for refinement |
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Similar 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: 40516.922 Da / Num. of mol.: 1 / Mutation: D79G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q51945, tartrate dehydrogenase, tartrate decarboxylase, D-malate dehydrogenase (decarboxylating) |
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#2: Chemical | ChemComp-NAI / |
#3: Chemical | ChemComp-NH4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 69.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.65 M ammonium sulfate, 0.2 M ammonium tartrate, 0.01 M DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 26, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 14251 / % possible obs: 84.7 % |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.3 % / % possible all: 80.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3FLK Resolution: 2.95→50 Å / Cor.coef. Fo:Fc: 0.871 / Cor.coef. Fo:Fc free: 0.822 / SU B: 18.902 / SU ML: 0.345 / Cross valid method: THROUGHOUT / ESU R: 0.793 / ESU R Free: 0.466 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.794 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.026 Å / Total num. of bins used: 20
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