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Yorodumi- PDB-5yuk: CO2 release in human carbonic anhydrase II crystals: reveal histi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yuk | ||||||||||||
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Title | CO2 release in human carbonic anhydrase II crystals: reveal histidine 64 and solvent dynamics | ||||||||||||
Components | Carbonic anhydrase 2 | ||||||||||||
Keywords | LYASE / Intermediate states | ||||||||||||
Function / homology | Function and homology information positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / one-carbon metabolic process / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||||||||
Authors | Kim, C.U. / Park, S.Y. / McKenna, R. | ||||||||||||
Funding support | United States, Korea, Republic Of, 3items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016 Title: Tracking solvent and protein movement during CO2 release in carbonic anhydrase II crystals. Authors: Kim, C.U. / Song, H. / Avvaru, B.S. / Gruner, S.M. / Park, S. / McKenna, R. #1: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016 Title: Tracking solvent and protein movement during CO2 release in carbonic anhydrase II crystals. Authors: Kim, C.U. / Song, H. / Avvaru, B.S. / Gruner, S.M. / Park, S. / McKenna, R. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yuk.cif.gz | 132 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yuk.ent.gz | 100.1 KB | Display | PDB format |
PDBx/mmJSON format | 5yuk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/5yuk ftp://data.pdbj.org/pub/pdb/validation_reports/yu/5yuk | HTTPS FTP |
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-Related structure data
Related structure data | 5dskC 5dslC 5dsmC 5dsoC 5dspC 5dsqC 5dsrC 5yuiC 5yujC 3d92S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29289.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-GOL / |
#4: 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: 2.07 Å3/Da / Density % sol: 40.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.3 M sodium citrate, 100 mM TrisHCl pH 7.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 23, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. obs: 40706 / % possible obs: 100 % / Redundancy: 7.4 % / Rsym value: 0.077 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.438 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3D92 Resolution: 1.45→24.52 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.65 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.049 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.984 Å2
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Refinement step | Cycle: 1 / Resolution: 1.45→24.52 Å
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Refine LS restraints |
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