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Yorodumi- PDB-7c5y: Crystal structure of the iota-carbonic anhydrase from eukaryotic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7c5y | ||||||
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Title | Crystal structure of the iota-carbonic anhydrase from eukaryotic microalga complexed with iodide | ||||||
Components | iota-carbonic anhydrase | ||||||
Keywords | LYASE / carbonic anhydrase / iodide complex | ||||||
Function / homology | IODIDE ION Function and homology information | ||||||
Biological species | Bigelowiella natans (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Senda, M. / Senda, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Bmc Biol. / Year: 2021 Title: Characterization of a novel type of carbonic anhydrase that acts without metal cofactors. Authors: Hirakawa, Y. / Senda, M. / Fukuda, K. / Yu, H.Y. / Ishida, M. / Taira, M. / Kinbara, K. / Senda, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7c5y.cif.gz | 228.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c5y.ent.gz | 164.1 KB | Display | PDB format |
PDBx/mmJSON format | 7c5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/7c5y ftp://data.pdbj.org/pub/pdb/validation_reports/c5/7c5y | HTTPS FTP |
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-Related structure data
Related structure data | 7c5vC 7c5wSC 7c5xC 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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Unit cell |
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-Components
#1: Protein | Mass: 55424.133 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bigelowiella natans (eukaryote) / Production host: Escherichia coli (E. coli) / References: carbonic anhydrase #2: Chemical | ChemComp-IOD / #3: 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: 2.35 Å3/Da / Density % sol: 47.75 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion Details: 20%(w/v) PEG4000, 20%(v/v) i-propanol, 0.1 M sodium citrate pH 5.6 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.9 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 2, 2019 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→49.6 Å / Num. obs: 101667 / % possible obs: 99 % / Redundancy: 7 % / Biso Wilson estimate: 20.31 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 14.56 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 7 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.17 / Num. unique obs: 14779 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MR native SAD phasing using 7C5W as a partial model Resolution: 2.2→49.6 Å / SU ML: 0.2117 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.7267 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: 22.73 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→49.6 Å
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Refine LS restraints |
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LS refinement shell |
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