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Yorodumi- PDB-6zxt: High resolution crystal structure of chloroplastic ribose-5-phosp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zxt | ||||||
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Title | High resolution crystal structure of chloroplastic ribose-5-phosphate isomerase from Chlamydomonas reinhardtii | ||||||
Components | Ribose-5-phosphate isomerase | ||||||
Keywords | ISOMERASE / Ribose-5-phosphate / Rossmann fold / enzyme / chloroplast / photosynthese / Chlamydomonas | ||||||
Function / homology | Ribose-5-phosphate isomerase, type A, subgroup / Ribose 5-phosphate isomerase, type A / Ribose 5-phosphate isomerase A (phosphoriboisomerase A) / ribose-5-phosphate isomerase / ribose-5-phosphate isomerase activity / pentose-phosphate shunt, non-oxidative branch / NagB/RpiA transferase-like / Ribose-5-phosphate isomerase Function and homology information | ||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å | ||||||
Authors | Le Moigne, T. / Crozet, P. / Lemaire, S.D. / Henri, J. | ||||||
Citation | Journal: Int J Mol Sci / Year: 2020 Title: High-Resolution Crystal Structure of Chloroplastic Ribose-5-Phosphate Isomerase from Chlamydomonas reinhardtii -An Enzyme Involved in the Photosynthetic Calvin-Benson Cycle. Authors: Le Moigne, T. / Crozet, P. / 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 | 6zxt.cif.gz | 192.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zxt.ent.gz | 152.5 KB | Display | PDB format |
PDBx/mmJSON format | 6zxt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/6zxt ftp://data.pdbj.org/pub/pdb/validation_reports/zx/6zxt | HTTPS FTP |
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-Related structure data
Related structure data | 6mc0S 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: 27587.811 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: RPI1, CHLRE_03g187450v5, CHLREDRAFT_55838 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: A8IRQ1, ribose-5-phosphate isomerase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal |
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Crystal grow |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→44.89 Å / Num. obs: 89012 / % possible obs: 99.62 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0519 / Rpim(I) all: 0.02114 / Rrim(I) all: 0.05611 / Net I/σ(I): 20.58 |
Reflection shell | Resolution: 1.404→1.454 Å / Rmerge(I) obs: 1.272 / Num. unique obs: 8611 / CC1/2: 0.382 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6MC0 Resolution: 1.4→44.89 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.79 / 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: 108.33 Å2 / Biso mean: 26.943 Å2 / Biso min: 13.63 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→44.89 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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