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Yorodumi- PDB-2p9e: Crystal Structure of G336V mutant of E.coli phosphoglycerate dehy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p9e | ||||||
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Title | Crystal Structure of G336V mutant of E.coli phosphoglycerate dehydrogenase | ||||||
Components | D-3-phosphoglycerate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / G336V mutant / 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: 2.6 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 | 2p9e.cif.gz | 315.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p9e.ent.gz | 258.7 KB | Display | PDB format |
PDBx/mmJSON format | 2p9e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/2p9e ftp://data.pdbj.org/pub/pdb/validation_reports/p9/2p9e | HTTPS FTP |
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-Related structure data
Related structure data | 2p9cC 2p9gC 2pa3SC 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 44140.449 Da / Num. of mol.: 4 / Mutation: G336V, C81A, C83A, C250A, C282A 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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-Non-polymers , 5 types, 101 molecules
#2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-NAI / #4: Chemical | ChemComp-CIT / #5: Chemical | ChemComp-SO4 / | #6: 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: 2.9 Å3/Da / Density % sol: 57.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.5M AmSO4, 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 16, 2005 / Details: Monochromator |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 61423 / % possible obs: 99.5 % / Redundancy: 18.7 % / Rmerge(I) obs: 0.165 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.846 / Mean I/σ(I) obs: 1.64 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2PA3 Resolution: 2.6→35 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.87 / SU B: 13.507 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R: 0.705 / ESU R Free: 0.345 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.904 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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