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Yorodumi- PDB-4nfy: Crystal Structure of 3-phosphoglycerate Dehydrogenase from Entamo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nfy | ||||||
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Title | Crystal Structure of 3-phosphoglycerate Dehydrogenase from Entamoeba histolytica | ||||||
Components | D-3-phosphoglycerate dehydrogenase, putative | ||||||
Keywords | OXIDOREDUCTASE / Rossmann Fold / Dehydrogenases | ||||||
Function / homology | Function and homology information phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / NAD binding / identical protein binding Similarity search - Function | ||||||
Biological species | Entamoeba histolytica (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Singh, R.K. / Gourinath, S. | ||||||
Citation | Journal: Febs J. / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nfy.cif.gz | 129.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nfy.ent.gz | 102 KB | Display | PDB format |
PDBx/mmJSON format | 4nfy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nfy_validation.pdf.gz | 440 KB | Display | wwPDB validaton report |
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Full document | 4nfy_full_validation.pdf.gz | 443.9 KB | Display | |
Data in XML | 4nfy_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 4nfy_validation.cif.gz | 32.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/4nfy ftp://data.pdbj.org/pub/pdb/validation_reports/nf/4nfy | HTTPS FTP |
-Related structure data
Related structure data | 4njmC 4njoC 1wwkS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Entamoeba histolytica (eukaryote) / Strain: HM-1-IMSS / Gene: 3-phosphoglycerate dehydrogenase, EHI_060860, EhPGDH / Plasmid: pET21c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q76KF5, phosphoglycerate dehydrogenase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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