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- PDB-2pa3: crystal structure of serine bound G336V mutant of E.coli phosphog... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2pa3 | ||||||
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Title | crystal structure of serine bound G336V mutant of E.coli phosphoglycerate dehydrogenase | ||||||
![]() | D-3-phosphoglycerate dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / phosphoglycerate dehydrogenase / serine biosynthesis | ||||||
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 | ![]() | 91.3 KB | Display | ![]() |
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PDB format | ![]() | 69.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 739.1 KB | Display | ![]() |
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Full document | ![]() | 752 KB | Display | |
Data in XML | ![]() | 17.8 KB | Display | |
Data in CIF | ![]() | 23.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2p9cC ![]() 2p9eC ![]() 2p9gC ![]() 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: 44140.449 Da / Num. of mol.: 1 / Mutation: C81A, C83A, C250A, C282A, G336V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SER / |
#3: Chemical | ChemComp-NAI / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 20% PEG1000, 0.1M Na/K phosphate, 0.2M MgCl2, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
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-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2005 / Details: monochromator |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.74→50 Å / Num. obs: 30270 / % possible obs: 99.9 % / Redundancy: 20.4 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 39.78 |
Reflection shell | Resolution: 2.74→2.84 Å / Redundancy: 16.4 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 5.23 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1PSD Resolution: 2.74→35 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.925 / SU B: 8.615 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.234 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.607 Å2
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Refinement step | Cycle: LAST / Resolution: 2.74→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.74→2.809 Å / Total num. of bins used: 20
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