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Yorodumi- PDB-4njm: Crystal Structure of phosphoglycerate bound 3-phosphoglycerate de... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4njm | ||||||
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Title | Crystal Structure of phosphoglycerate bound 3-phosphoglycerate dehydrogenase in Entamoeba histolytica | ||||||
Components | (D-3-phosphoglycerate dehydrogenase, putative) x 2 | ||||||
Keywords | OXIDOREDUCTASE / Rossmann Fold / Dehydrogenase | ||||||
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: 1.79 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 | 4njm.cif.gz | 138.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4njm.ent.gz | 107 KB | Display | PDB format |
PDBx/mmJSON format | 4njm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/4njm ftp://data.pdbj.org/pub/pdb/validation_reports/nj/4njm | HTTPS FTP |
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-Related structure data
Related structure data | 4nfySC 4njoC C: citing same article (ref.) S: Starting model for refinement |
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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: 34749.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM1:IMSS / Gene: EhPGDH, EHI_060860 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q76KF5, phosphoglycerate dehydrogenase | ||
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#2: Protein | Mass: 34825.566 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM1:IMSS / Gene: EhPGDH, EHI_060860 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q76KF5, phosphoglycerate dehydrogenase | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.38 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25% PEG 3350, 100mM Tris pH 7.0-8.0, 200mM sodium formate, 5% glycerol , 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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 20, 2011 |
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→88.03 Å / Num. obs: 63428 / % possible obs: 99.9 % |
Reflection shell | Resolution: 1.8→1.83 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NFY Resolution: 1.79→88.03 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.761 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 31.388 Å2
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Refinement step | Cycle: LAST / Resolution: 1.79→88.03 Å
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Refine LS restraints |
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