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Yorodumi- PDB-7zy7: Crystal structure of Chlamydomonas reinhardtii chloroplastic phos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zy7 | ||||||
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Title | Crystal structure of Chlamydomonas reinhardtii chloroplastic phosphoglycerate kinase | ||||||
Components | Phosphoglycerate kinase | ||||||
Keywords | PHOTOSYNTHESIS | ||||||
Function / homology | Function and homology information phosphoglycerate kinase / phosphoglycerate kinase activity / gluconeogenesis / glycolytic process / ADP binding / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å | ||||||
Authors | Le Moigne, T. / Lemaire, S.D. / Henri, J. | ||||||
Funding support | France, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Chlamydomonas reinhardtii chloroplastic phosphoglycerate kinase Authors: Le Moigne, T. / Lemaire, S.D. / Henri, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zy7.cif.gz | 169.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zy7.ent.gz | 131.6 KB | Display | PDB format |
PDBx/mmJSON format | 7zy7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zy7_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7zy7_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7zy7_validation.xml.gz | 32.5 KB | Display | |
Data in CIF | 7zy7_validation.cif.gz | 48 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/7zy7 ftp://data.pdbj.org/pub/pdb/validation_reports/zy/7zy7 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 43933.645 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: PGK1, CHLRE_11g467770v5, CHLREDRAFT_132210 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A8JC04, phosphoglycerate kinase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.09 Å3/Da / Density % sol: 41.05 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 100 mM MES pH 5, 20% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980115 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 1, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.980115 Å / Relative weight: 1 |
Reflection | Resolution: 1.975→42.16 Å / Num. obs: 50948 / % possible obs: 99.31 % / Redundancy: 6.9 % / CC1/2: 0.994 / CC star: 0.998 / Net I/σ(I): 9.98 |
Reflection shell | Resolution: 1.975→2.046 Å / Mean I/σ(I) obs: 1.18 / Num. unique obs: 4838 / CC1/2: 0.354 / CC star: 0.723 / % possible all: 93.38 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Alphafold model Resolution: 1.98→42.16 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.71 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.68 Å2 / Biso mean: 34.1276 Å2 / Biso min: 14.95 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.98→42.16 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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