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Yorodumi- PDB-7b1w: Crystal structure of plastidial ribulose epimerase RPE1 from the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7b1w | ||||||||||||
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Title | Crystal structure of plastidial ribulose epimerase RPE1 from the model alga Chlamydomonas reinhardtii | ||||||||||||
Components | Ribulose-phosphate 3-epimerasePhosphopentose epimerase | ||||||||||||
Keywords | ISOMERASE / Calvin-Benson cycle / photosynthesis / ribulose / ribose / epimerase / chloroplast / carbon fixation | ||||||||||||
Function / homology | Function and homology information : / ribulose-phosphate 3-epimerase / D-ribulose-phosphate 3-epimerase activity / stromule / pentose catabolic process / pentose-phosphate shunt, non-oxidative branch / response to nematode / thylakoid / apoplast / chloroplast envelope ...: / ribulose-phosphate 3-epimerase / D-ribulose-phosphate 3-epimerase activity / stromule / pentose catabolic process / pentose-phosphate shunt, non-oxidative branch / response to nematode / thylakoid / apoplast / chloroplast envelope / chloroplast stroma / response to cold / metal ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.935 Å | ||||||||||||
Authors | Henri, J. / Zaffagnini, M. / Tedesco, D. / Crozet, P. / Lemaire, S.D. | ||||||||||||
Funding support | France, 3items
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Citation | Journal: Plant Physiol. / Year: 2023 Title: Characterization of chloroplast ribulose-5-phosphate-3-epimerase from the microalga Chlamydomonas reinhardtii. Authors: Meloni, M. / Fanti, S. / Tedesco, D. / Gurrieri, L. / Trost, P. / Fermani, S. / Lemaire, S.D. / Zaffagnini, M. / Henri, J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b1w.cif.gz | 552.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b1w.ent.gz | 450.8 KB | Display | PDB format |
PDBx/mmJSON format | 7b1w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/7b1w ftp://data.pdbj.org/pub/pdb/validation_reports/b1/7b1w | HTTPS FTP |
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-Related structure data
-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
#1: Protein | Mass: 26811.033 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: RPE1, CHLRE_12g511900v5, CHLREDRAFT_135614 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A8IKW6, ribulose-phosphate 3-epimerase #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.4 Å3/Da / Density % sol: 48.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Calcium acetate 160 mmol/L Sodium cacodylate pH 6.5 80 mmol/L Glycerol 20 % Polyethylene glycol 8000 14.4 % |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.935→49.29 Å / Num. obs: 229414 / % possible obs: 98.65 % / Redundancy: 7.2 % / Biso Wilson estimate: 30.3 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.79 |
Reflection shell | Resolution: 1.935→2.005 Å / Num. unique obs: 21621 / CC1/2: 0.616 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Homology model Resolution: 1.935→49.289 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.56 / 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: 83.91 Å2 / Biso mean: 34.7765 Å2 / Biso min: 15.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.935→49.289 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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