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- PDB-4nfy: Crystal Structure of 3-phosphoglycerate Dehydrogenase from Entamo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4nfy | ||||||
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Title | Crystal Structure of 3-phosphoglycerate Dehydrogenase from Entamoeba histolytica | ||||||
![]() | D-3-phosphoglycerate dehydrogenase, putative | ||||||
![]() | OXIDOREDUCTASE / Rossmann Fold / Dehydrogenases | ||||||
Function / homology | ![]() phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / NAD binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Singh, R.K. / Gourinath, S. | ||||||
![]() | ![]() Title: Crystal structures and kinetics of Type III 3-phosphoglycerate dehydrogenase reveal catalysis by lysine. Authors: Singh, R.K. / Raj, I. / Pujari, R. / Gourinath, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129.4 KB | Display | ![]() |
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PDB format | ![]() | 102 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440 KB | Display | ![]() |
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Full document | ![]() | 443.9 KB | Display | |
Data in XML | ![]() | 23.4 KB | Display | |
Data in CIF | ![]() | 32.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4njmC ![]() 4njoC ![]() 1wwkS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34591.293 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.41 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG, 100mM Tris-cl, 350mM sodium formate, 5% Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 77.15 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 20, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→85.91 Å / Num. obs: 22458 / Redundancy: 4.2 % / Rsym value: 0.047 / Net I/σ(I): 36.4 |
Reflection shell | Resolution: 2.45→2.49 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 7.4 / Rsym value: 0.202 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1WWK Resolution: 2.45→85.91 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.914 / SU B: 9.961 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R: 0.803 / ESU R Free: 0.31 / 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: 48.265 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→85.91 Å
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Refine LS restraints |
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