+Open data
-Basic information
Entry | Database: PDB / ID: 3a12 | ||||||
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Title | Crystal structure of Type III Rubisco complexed with 2-CABP | ||||||
Components | Ribulose bisphosphate carboxylaseRuBisCO | ||||||
Keywords | LYASE / ribulose-1 / 5-bisphosphate carboxylase/oxygenase / Rubisco / Carbon dioxide fixation / Magnesium / Metal-binding / Monooxygenase / Oxidoreductase | ||||||
Function / homology | Function and homology information AMP catabolic process / ribulose-bisphosphate carboxylase / carbon fixation / ribulose-bisphosphate carboxylase activity / oxidoreductase activity / magnesium ion binding Similarity search - Function | ||||||
Biological species | Pyrococcus kodakaraensis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Nishitani, Y. / Fujihashi, M. / Doi, T. / Yoshida, S. / Atomi, H. / Imanaka, T. / Miki, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Structure-based catalytic optimization of a type III Rubisco from a hyperthermophile Authors: Nishitani, Y. / Yoshida, S. / Fujihashi, M. / Kitagawa, K. / Doi, T. / Atomi, H. / Imanaka, T. / Miki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a12.cif.gz | 872.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a12.ent.gz | 724.3 KB | Display | PDB format |
PDBx/mmJSON format | 3a12.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/3a12 ftp://data.pdbj.org/pub/pdb/validation_reports/a1/3a12 | HTTPS FTP |
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-Related structure data
Related structure data | 3kdnC 3kdoC 1gehS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 49819.480 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus kodakaraensis (archaea) / Strain: KOD1 / Gene: rbcL, TK2290 / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS References: UniProt: O93627, ribulose-bisphosphate carboxylase #2: Chemical | ChemComp-MG / #3: Sugar | ChemComp-CAP / #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: 3.1 Å3/Da / Density % sol: 60.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M Acetate, 0.1M CaCl2, 5% PEG6000, 10% MPD, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 4, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 271962 / % possible obs: 99.9 % / Biso Wilson estimate: 26.4 Å2 / Rsym value: 0.105 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.3→2.34 Å / Mean I/σ(I) obs: 3.9 / Rsym value: 0.379 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GEH Resolution: 2.3→35.39 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.948 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.083 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→35.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.302→2.362 Å / Total num. of bins used: 20
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