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Yorodumi- PDB-6kyj: Hybrid-Rubisco (rice RbcL and sorghum RbcS) in complex with sulfa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kyj | |||||||||||||||
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Title | Hybrid-Rubisco (rice RbcL and sorghum RbcS) in complex with sulfate ions | |||||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / CO2 assimilation / C4 plant / rice / Rubisco | |||||||||||||||
Function / homology | Function and homology information photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / plastid / chloroplast / monooxygenase activity / magnesium ion binding Similarity search - Function | |||||||||||||||
Biological species | Oryza sativa (Asian cultivated rice) Sorghum bicolor (sorghum) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||||||||
Authors | Matsumura, H. / Yoshizawa, T. / Tanaka, S. / Yoshikawa, H. | |||||||||||||||
Funding support | Japan, 4items
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Citation | Journal: Mol Plant / Year: 2020 Title: Hybrid Rubisco with Complete Replacement of Rice Rubisco Small Subunits by Sorghum Counterparts Confers C 4 Plant-like High Catalytic Activity. Authors: Matsumura, H. / Shiomi, K. / Yamamoto, A. / Taketani, Y. / Kobayashi, N. / Yoshizawa, T. / Tanaka, S.I. / Yoshikawa, H. / Endo, M. / Fukayama, H. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kyj.cif.gz | 599.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kyj.ent.gz | 393.9 KB | Display | PDB format |
PDBx/mmJSON format | 6kyj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/6kyj ftp://data.pdbj.org/pub/pdb/validation_reports/ky/6kyj | HTTPS FTP |
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-Related structure data
Related structure data | 6kyiC 3axmS 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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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 52950.027 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: rbcL, PA064 / Production host: Escherichia coli (E. coli) References: UniProt: P0C510, ribulose-bisphosphate carboxylase #2: Protein | Mass: 19110.840 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sorghum bicolor (sorghum) / Gene: RbcS / Production host: Escherichia coli (E. coli) References: UniProt: E3WDK7, ribulose-bisphosphate carboxylase #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: 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: 2.37 Å3/Da / Density % sol: 48.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Tris-HCl (pH 9.0), 0.2M lithium sulfate, 15%(w/v) polyethylene glycol 4000, and 10 %(w/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→48.58 Å / Num. obs: 299765 / % possible obs: 99.98 % / Redundancy: 27.2 % / Biso Wilson estimate: 20.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1184 / Rpim(I) all: 0.02303 / Rrim(I) all: 0.1207 / Net I/σ(I): 23.31 |
Reflection shell | Resolution: 1.7→1.761 Å / Rmerge(I) obs: 1.138 / Mean I/σ(I) obs: 3.13 / Num. unique obs: 29707 / CC1/2: 0.82 / Rpim(I) all: 0.2335 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AXM Resolution: 1.7→48.58 Å / SU ML: 0.1591 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.1838
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.26 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→48.58 Å
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Refine LS restraints |
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LS refinement shell |
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