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Yorodumi- PDB-6h7g: Crystal structure of redox-sensitive phosphoribulokinase (PRK) fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h7g | ||||||
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Title | Crystal structure of redox-sensitive phosphoribulokinase (PRK) from the green algae Chlamydomonas reinhardtii | ||||||
Components | Phosphoribulokinase, chloroplastic | ||||||
Keywords | PHOTOSYNTHESIS / Transferase / ATP binding / kinase activity | ||||||
Function / homology | Function and homology information phosphoribulokinase / phosphoribulokinase activity / supramolecular complex / stromule / reductive pentose-phosphate cycle / response to cold / chloroplast / disordered domain specific binding / phosphorylation / enzyme binding ...phosphoribulokinase / phosphoribulokinase activity / supramolecular complex / stromule / reductive pentose-phosphate cycle / response to cold / chloroplast / disordered domain specific binding / phosphorylation / enzyme binding / protein homodimerization activity / ATP binding Similarity search - Function | ||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Fermani, S. / Sparla, F. / Gurrieri, L. / Demitri, N. / Polentarutti, M. / Falini, G. / Trost, P. / Lemaire, S.D. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: ArabidopsisandChlamydomonasphosphoribulokinase crystal structures complete the redox structural proteome of the Calvin-Benson cycle. Authors: Gurrieri, L. / Del Giudice, A. / Demitri, N. / Falini, G. / Pavel, N.V. / Zaffagnini, M. / Polentarutti, M. / Crozet, P. / Marchand, C.H. / Henri, J. / Trost, P. / Lemaire, S.D. / Sparla, F. / Fermani, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6h7g.cif.gz | 143 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h7g.ent.gz | 112.7 KB | Display | PDB format |
PDBx/mmJSON format | 6h7g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/6h7g ftp://data.pdbj.org/pub/pdb/validation_reports/h7/6h7g | HTTPS FTP |
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-Related structure data
Related structure data | 6h7hC 5b3fS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38813.543 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: PRKA / Organ: chloroplast / Plasmid: pET-28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19824, phosphoribulokinase #2: Chemical | #3: 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: 2.65 Å3/Da / Density % sol: 53.6 % / Description: needle-like |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 22 % w/v PEG MME 5K, 0.1 M MES, pH 6.5, 0.2 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.24 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 15, 2015 |
Radiation | Monochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.24 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→44.38 Å / Num. obs: 27230 / % possible obs: 99.6 % / Observed criterion σ(F): 3 / Redundancy: 5.1 % / Biso Wilson estimate: 58.95 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3280 / CC1/2: 0.743 / Rsym value: 0.77 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5B3F Resolution: 2.6→39.859 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.86
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→39.859 Å
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Refine LS restraints |
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LS refinement shell |
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