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Yorodumi- PDB-1ir1: Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ir1 | |||||||||
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Title | Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with CO2, Mg2+ and 2-Carboxyarabinitol-1,5-Bisphosphate | |||||||||
Components |
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Keywords | LYASE / ALPHA/BETA BARREL | |||||||||
Function / homology | Function and homology information photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / chloroplast / magnesium ion binding Similarity search - Function | |||||||||
Biological species | Spinacia oleracea (spinach) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / RE-REFINEMENT of 1BUR / Resolution: 1.8 Å | |||||||||
Authors | Mizohata, E. / Matsumura, H. / Okano, Y. / Kumei, M. / Takuma, H. / Onodera, J. / Kato, K. / Shibata, N. / Inoue, T. / Yokota, A. / Kai, Y. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Crystal structure of activated ribulose-1,5-bisphosphate carboxylase/oxygenase from green alga Chlamydomonas reinhardtii complexed with 2-carboxyarabinitol-1,5-bisphosphate. Authors: Mizohata, E. / Matsumura, H. / Okano, Y. / Kumei, M. / Takuma, H. / Onodera, J. / Kato, K. / Shibata, N. / Inoue, T. / Yokota, A. / Kai, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ir1.cif.gz | 512.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ir1.ent.gz | 416.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ir1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ir1_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 1ir1_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 1ir1_validation.xml.gz | 108.5 KB | Display | |
Data in CIF | 1ir1_validation.cif.gz | 157.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ir/1ir1 ftp://data.pdbj.org/pub/pdb/validation_reports/ir/1ir1 | HTTPS FTP |
-Related structure data
Related structure data | 1ir2C 1bur C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a hexadecamer comprised of 8 large and 8 small subunits. A half of the hexadecamer (4 large and 4 small subunits) exists in the asymmetric unit. The rest part is generated by -x, y, -z+1/2. |
-Components
#1: Protein | Mass: 52849.742 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / Organ: leaves References: UniProt: P00875, ribulose-bisphosphate carboxylase #2: Protein | Mass: 14687.708 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / Organ: leaves References: UniProt: Q43832, ribulose-bisphosphate carboxylase #3: Chemical | ChemComp-MG / #4: Sugar | ChemComp-CAP / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.84 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.9 Details: PEG4000, MgCl2, NaHCO3, DTT, 2-carboxyarabinitol-1,5-bisphosphate, Bicine, pH 7.9, VAPOR DIFFUSION, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.8→10 Å / Num. obs: 175568 / % possible obs: 76.9 % |
Reflection shell | Resolution: 1.8→1.86 Å / Num. unique all: 10760 / % possible all: 47.5 |
-Processing
Software | Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||
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Refinement | Method to determine structure: RE-REFINEMENT of 1BUR Starting model: PDB ID 1BUR 1bur Resolution: 1.8→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree error: 0.013
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Refinement | *PLUS Rfactor Rfree: 0.179 / Rfactor Rwork: 0.155 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.8 Å / Rfactor Rfree: 0.304 / Rfactor Rwork: 0.282 |