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- PDB-2p9g: Crystal structure of serine bound G336V,G337V double mutant of E.... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2p9g | ||||||
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Title | Crystal structure of serine bound G336V,G337V double mutant of E.coli phosphoglycerate dehydrogenase | ||||||
![]() | D-3-phosphoglycerate dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / serine biosynthesis / D-3-phosphoglycerate dehydrogenase / double mutation | ||||||
Function / homology | ![]() 2-hydroxyglutarate dehydrogenase activity / 2-oxoglutarate reductase / phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / NADH binding / L-serine biosynthetic process / serine binding / NAD+ binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Dey, S. / Sacchettini, J.C. | ||||||
![]() | ![]() Title: The Effect of Hinge Mutations on Effector Binding and Domain Rotation in Escherichia coli D-3-Phosphoglycerate Dehydrogenase. Authors: Dey, S. / Hu, Z. / Xu, X.L. / Sacchettini, J.C. / Grant, G.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 | ![]() | 165.5 KB | Display | ![]() |
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PDB format | ![]() | 131.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 962.2 KB | Display | ![]() |
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Full document | ![]() | 989.4 KB | Display | |
Data in XML | ![]() | 33.6 KB | Display | |
Data in CIF | ![]() | 44.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2p9cC ![]() 2p9eC ![]() 2pa3C ![]() 1psdS C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 44182.527 Da / Num. of mol.: 2 / Mutation: C81A, C83A, C250A, C282A, G336V, G337V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.41 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 30% PEG 400, 0.1M acetate, 0.2M Calcium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction source | Source: ![]() |
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Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 9, 2006 / Details: monochromator |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→40.32 Å / Num. obs: 25289 / % possible obs: 99.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 4.8 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1PSD Resolution: 2.8→35 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.911 / SU B: 13.366 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R Free: 0.366 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.721 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.872 Å / Total num. of bins used: 20
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