+Open data
-Basic information
Entry | Database: PDB / ID: 1iwa | ||||||
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Title | RUBISCO FROM GALDIERIA PARTITA | ||||||
Components |
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Keywords | LYASE / RUBISCO / PHOTOSYNTHESIS | ||||||
Function / homology | Function and homology information ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / chloroplast / magnesium ion binding Similarity search - Function | ||||||
Biological species | Galdieria partita (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å | ||||||
Authors | Okano, Y. / Mizohata, E. / Xie, Y. / Matsumura, H. / Sugawara, H. / Inoue, T. / Yokota, A. / Kai, Y. | ||||||
Citation | Journal: FEBS LETT. / Year: 2002 Title: X-Ray Structure of Galdieria Rubisco Complexed with one sulfate ion per active site Authors: Okano, Y. / Mizohata, E. / Xie, Y. / Matsumura, H. / Sugawara, H. / Inoue, T. / Yokota, A. / Kai, Y. #1: Journal: J.Mol.Biol. / Year: 2000 Title: The Transition between the Open and Closed States of Rubisco is triggered by the Inter-Phosphate Distance of the Bound Bisphosphate Authors: Duff, A.P. / Andrews, T.J. / Curmi, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iwa.cif.gz | 1003.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iwa.ent.gz | 829.9 KB | Display | PDB format |
PDBx/mmJSON format | 1iwa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1iwa_validation.pdf.gz | 579.9 KB | Display | wwPDB validaton report |
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Full document | 1iwa_full_validation.pdf.gz | 723.2 KB | Display | |
Data in XML | 1iwa_validation.xml.gz | 214.3 KB | Display | |
Data in CIF | 1iwa_validation.cif.gz | 300.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/1iwa ftp://data.pdbj.org/pub/pdb/validation_reports/iw/1iwa | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 55058.746 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Galdieria partita (eukaryote) References: UniProt: O98949, ribulose-bisphosphate carboxylase #2: Protein | Mass: 16211.486 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Galdieria partita (eukaryote) References: UniProt: O98950, ribulose-bisphosphate carboxylase #3: Chemical | ChemComp-SO4 / #4: 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: 2.45 Å3/Da / Density % sol: 49.31 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Biso Wilson estimate: 29.9 Å2 |
Reflection shell | Resolution: 2.6→40 Å |
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 40.8 Å / Num. obs: 172258 / % possible obs: 98.9 % / Num. measured all: 895084 / Rmerge(I) obs: 0.103 |
Reflection shell | *PLUS Lowest resolution: 2.76 Å / % possible obs: 97.4 % / Rmerge(I) obs: 0.306 |
-Processing
Software |
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Refinement | Resolution: 2.6→25.65 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.6045 Å2 / ksol: 0.38453 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.9 Å2
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Refine analyze | Luzzati coordinate error free: 0.33 Å / Luzzati sigma a free: 0.38 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→25.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 40 Å / Num. reflection obs: 172258 / % reflection Rfree: 5 % | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.6 Å |