+Open data
-Basic information
Entry | Database: PDB / ID: 5y2r | ||||||||||||
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Title | 2.5 atm CO2-pressurized human carbonic anhydrase II | ||||||||||||
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 Å | ||||||||||||
Authors | Kim, C.U. / Park, S.Y. | ||||||||||||
Funding support | Korea, Republic Of, 3items
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Citation | Journal: IUCrJ / Year: 2018 Title: Active-site solvent replenishment observed during human carbonic anhydrase II catalysis. Authors: Kim, J.K. / Lomelino, C.L. / Avvaru, B.S. / Mahon, B.P. / McKenna, R. / Park, S. / Kim, C.U. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y2r.cif.gz | 142.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y2r.ent.gz | 108.6 KB | Display | PDB format |
PDBx/mmJSON format | 5y2r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/5y2r ftp://data.pdbj.org/pub/pdb/validation_reports/y2/5y2r | HTTPS FTP |
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-Related structure data
Related structure data | 5y2sC 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-CO2 / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Sequence details | In chain A, residue number 126 is simply skipped. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / 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: F1 / Wavelength: 0.918 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 16, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1→30 Å / Num. obs: 122146 / % possible obs: 98.6 % / Redundancy: 7.1 % / Net I/σ(I): 25.1 |
Reflection shell | Resolution: 1→1.02 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 3 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3D92 Resolution: 1→17.48 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.458 / SU ML: 0.011 / Cross valid method: THROUGHOUT / ESU R: 0.019 / ESU R Free: 0.02 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.893 Å2
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Refinement step | Cycle: 1 / Resolution: 1→17.48 Å
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Refine LS restraints |
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