+Open data
-Basic information
Entry | Database: PDB / ID: 7t1c | ||||||
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Title | Crystal structure of RUBISCO from Sulfurivirga caldicuralii | ||||||
Components | Ribulose-bisphosphate carboxylaseRuBisCO | ||||||
Keywords | LYASE / Ribulose-1 / 5-bisphosphate carboxylase-oxygenase | ||||||
Function / homology | Function and homology information ribulose-bisphosphate carboxylase / carbon fixation / ribulose-bisphosphate carboxylase activity / magnesium ion binding Similarity search - Function | ||||||
Biological species | Sulfurivirga caldicuralii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Pereira, J.H. / Liu, A.K. / Shih, P.M. / Adams, P.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Adv / Year: 2022 Title: Structural plasticity enables evolution and innovation of RuBisCO assemblies. Authors: Liu, A.K. / Pereira, J.H. / Kehl, A.J. / Rosenberg, D.J. / Orr, D.J. / Chu, S.K.S. / Banda, D.M. / Hammel, M. / Adams, P.D. / Siegel, J.B. / Shih, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7t1c.cif.gz | 322.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t1c.ent.gz | 221.7 KB | Display | PDB format |
PDBx/mmJSON format | 7t1c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t1/7t1c ftp://data.pdbj.org/pub/pdb/validation_reports/t1/7t1c | HTTPS FTP |
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-Related structure data
Related structure data | 7t1jC 6iusS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 51722.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfurivirga caldicuralii (bacteria) / Gene: SAMN05443662_0203 / Production host: Escherichia coli (E. coli) References: UniProt: A0A1N6DK16, ribulose-bisphosphate carboxylase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.05 M Citric acid, 0.05 M Bis-TRIS propane pH 5.0, 16 % PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→43.55 Å / Num. obs: 61467 / % possible obs: 100 % / Redundancy: 19.4 % / Biso Wilson estimate: 27.6 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.73→1.79 Å / Num. unique obs: 6044 / CC1/2: 0.35 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IUS Resolution: 1.73→43.55 Å / SU ML: 0.1858 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.029 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73→43.55 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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