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Yorodumi- PDB-6h7h: Crystal structure of redox-sensitive phosphoribulokinase (PRK) fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h7h | |||||||||
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Title | Crystal structure of redox-sensitive phosphoribulokinase (PRK) from Arabidopsis thaliana | |||||||||
Components | Phosphoribulokinase, chloroplastic | |||||||||
Keywords | PHOTOSYNTHESIS / Transferase / kinase / ATP binding | |||||||||
Function / homology | Function and homology information phosphoribulokinase / phosphoribulokinase activity / supramolecular complex / stromule / apoplast / reductive pentose-phosphate cycle / chloroplast envelope / thylakoid / chloroplast stroma / chloroplast thylakoid membrane ...phosphoribulokinase / phosphoribulokinase activity / supramolecular complex / stromule / apoplast / reductive pentose-phosphate cycle / chloroplast envelope / thylakoid / chloroplast stroma / chloroplast thylakoid membrane / response to cold / chloroplast / disordered domain specific binding / phosphorylation / protein homodimerization activity / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.471 Å | |||||||||
Authors | Fermani, S. / Sparla, F. / Gurrieri, L. / Falini, G. / Trost, P. | |||||||||
Funding support | Italy, 2items
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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 | 6h7h.cif.gz | 144.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h7h.ent.gz | 113.6 KB | Display | PDB format |
PDBx/mmJSON format | 6h7h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/6h7h ftp://data.pdbj.org/pub/pdb/validation_reports/h7/6h7h | HTTPS FTP |
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-Related structure data
Related structure data | 6h7gSC S: Starting model for refinement C: citing same article (ref.) |
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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: 39511.871 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g32060, T12O21.4 / Organ: chloroplast / Plasmid: pET-28 / Organ (production host): chloroplast / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25697, phosphoribulokinase #2: 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 Å3/Da / Density % sol: 39.4 % / Description: bipiramidal |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 1.5 M sodium malonate, pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 15, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 |
Reflection | Resolution: 2.47→82.23 Å / Num. obs: 24824 / % possible obs: 97.6 % / Observed criterion σ(F): 3 / Redundancy: 6.9 % / Biso Wilson estimate: 52.5 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.47→2.58 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3107 / CC1/2: 0.947 / Rsym value: 0.435 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6H7G Resolution: 2.471→46.76 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 38.95
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.471→46.76 Å
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Refine LS restraints |
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LS refinement shell |
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