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Yorodumi- PDB-4njo: crystal structure of cofactor(NAD+) bound 3-phosphoglycerate dehy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4njo | ||||||
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Title | crystal structure of cofactor(NAD+) bound 3-phosphoglycerate dehydrogenase in Entamoeba histolytica | ||||||
Components | D-3-phosphoglycerate dehydrogenase, putative | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.22 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 | 4njo.cif.gz | 131.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4njo.ent.gz | 102.2 KB | Display | PDB format |
PDBx/mmJSON format | 4njo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/4njo ftp://data.pdbj.org/pub/pdb/validation_reports/nj/4njo | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 34749.449 Da / Num. of mol.: 2 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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-Non-polymers , 5 types, 153 molecules
#2: Chemical | ChemComp-NAD / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-TRS / | #5: Chemical | ChemComp-GOL / | #6: 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: 1.94 Å3/Da / Density % sol: 36.47 % |
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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 300mM sodium formate, 5% glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 15, 2012 |
Radiation | Monochromator: Cu-Ni / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→52.09 Å / Num. obs: 24702 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.22→2.3 Å / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→52.09 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 7.397 / SU ML: 0.187 / SU R Cruickshank DPI: 0.5288 / Cross valid method: THROUGHOUT / ESU R: 0.532 / ESU R Free: 0.259 / 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: 45.223 Å2
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Refinement step | Cycle: LAST / Resolution: 2.22→52.09 Å
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Refine LS restraints |
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