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Open data
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Basic information
Entry | Database: PDB / ID: 7y2a | ||||||
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Title | Zn-Carbonic Anhydrase II complexed with 3NPA before UV at 90 K | ||||||
![]() | Carbonic anhydrase 2 | ||||||
![]() | METAL BINDING PROTEIN / Carbonic Anhydrase / enzyme mechanism / metalloenzymes | ||||||
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 / carbonic anhydrase / regulation of intracellular pH / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, C.U. / Kim, J.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Temperature series of human Carbonic Anhydrase II with photolysis of caged CO2 Authors: Kim, C.U. / Kim, J.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.9 KB | Display | ![]() |
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PDB format | ![]() | 99.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 22 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7y2cC ![]() 7y2eC ![]() 7y2fC ![]() 7y2gC ![]() 7y2hC ![]() 7y2iC ![]() 7y2jC ![]() 7y2kC ![]() 7y2lC ![]() 7y2mC ![]() 7y2nC ![]() 7y2oC ![]() 7y2qC ![]() 7y2rC ![]() 7y2sC ![]() 7y2tC ![]() 7y2uC ![]() 7y2vC ![]() 7y2wC ![]() 7y2xC ![]() 6luwS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 | ChemComp-MNP / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.3 M sodium citrate, 50 mM Tris-HCl |
-Data collection
Diffraction | Mean temperature: 90 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Dec 2, 2019 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→30 Å / Num. obs: 72324 / % possible obs: 96.1 % / Redundancy: 3.8 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.027 / Rrim(I) all: 0.053 / Net I/σ(I): 29.2 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 6.4 / Num. unique obs: 3482 / CC1/2: 0.961 / CC star: 0.99 / Rpim(I) all: 0.114 / Rrim(I) all: 0.225 / % possible all: 93.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6LUW Resolution: 1.2→29.05 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.932 / SU ML: 0.02 / Cross valid method: FREE R-VALUE / ESU R: 0.035 / ESU R Free: 0.036 / 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: 12.026 Å2
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Refinement step | Cycle: 1 / Resolution: 1.2→29.05 Å
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Refine LS restraints |
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