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- PDB-5yui: CO2 release in human carbonic anhydrase II crystals: reveal histi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5yui | ||||||||||||
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Title | CO2 release in human carbonic anhydrase II crystals: reveal histidine 64 and solvent dynamics | ||||||||||||
![]() | Carbonic anhydrase 2 | ||||||||||||
![]() | LYASE / Intermediate states | ||||||||||||
Function / homology | ![]() 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 / morphogenesis of an epithelium / regulation of intracellular pH / 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 / zinc ion binding / extracellular exosome / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Kim, C.U. / Park, S.Y. / McKenna, R. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 137.9 KB | Display | ![]() |
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PDB format | ![]() | 104.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 25.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5dskC ![]() 5dslC ![]() 5dsmC ![]() 5dsoC ![]() 5dspC ![]() 5dsqC ![]() 5dsrC ![]() 5yujC ![]() 5yukC ![]() 3d92S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-ZN / | ||||
#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.3M sodium citrate, 100mM TrisHCl pH 7.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 21, 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: 1.2→50 Å / Num. obs: 69247 / % possible obs: 96 % / Redundancy: 6.7 % / Rsym value: 0.056 / Net I/σ(I): 30.4 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.596 / % possible all: 65.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3D92 Resolution: 1.2→26.72 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.966 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.032 / 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: 13.961 Å2
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Refinement step | Cycle: 1 / Resolution: 1.2→26.72 Å
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Refine LS restraints |
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