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Yorodumi- PDB-2pa3: crystal structure of serine bound G336V mutant of E.coli phosphog... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pa3 | ||||||
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Title | crystal structure of serine bound G336V mutant of E.coli phosphoglycerate dehydrogenase | ||||||
Components | D-3-phosphoglycerate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / phosphoglycerate dehydrogenase / serine biosynthesis | ||||||
Function / homology | Function and homology information 2-hydroxyglutarate dehydrogenase activity / 2-oxoglutarate reductase / phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / serine binding / NADH binding / L-serine biosynthetic process / NAD+ binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å | ||||||
Authors | Dey, S. / Sacchettini, J.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pa3.cif.gz | 91.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pa3.ent.gz | 69.5 KB | Display | PDB format |
PDBx/mmJSON format | 2pa3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pa/2pa3 ftp://data.pdbj.org/pub/pdb/validation_reports/pa/2pa3 | HTTPS FTP |
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-Related structure data
Related structure data | 2p9cC 2p9eC 2p9gC 1psdS 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: 44140.449 Da / Num. of mol.: 1 / Mutation: C81A, C83A, C250A, C282A, G336V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: serA / Plasmid: pTrc99 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P0A9T0, phosphoglycerate dehydrogenase |
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#2: Chemical | ChemComp-SER / |
#3: Chemical | ChemComp-NAI / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9795 Å |
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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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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