[English] 日本語
![](img/lk-miru.gif)
- PDB-3cyu: Human Carbonic Anhydrase II complexed with Cryptophane biosensor ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3cyu | ||||||
---|---|---|---|---|---|---|---|
Title | Human Carbonic Anhydrase II complexed with Cryptophane biosensor and xenon | ||||||
![]() | Carbonic anhydrase 2 | ||||||
![]() | LYASE / Zinc metalloenzyme / sulfonamide / cryptophane / xenon / biosensor / Disease mutation / Metal-binding | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Aaron, J.A. / Jude, K.M. / Di Costanzo, L. / Christianson, D.W. | ||||||
![]() | ![]() Title: Structure of a 129Xe-cryptophane biosensor complexed with human carbonic anhydrase II. Authors: Aaron, J.A. / Chambers, J.M. / Jude, K.M. / Di Costanzo, L. / Dmochowski, I.J. / Christianson, D.W. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 79.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 55.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 918.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 954.5 KB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 26.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1lg6S S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29289.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 190 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/0CR.gif)
![](data/chem/img/1CR.gif)
![](data/chem/img/XE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/0CR.gif)
![](data/chem/img/1CR.gif)
![](data/chem/img/XE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||
---|---|---|---|
#3: Chemical | ChemComp-0CR / | ||
#4: Chemical | ChemComp-1CR / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.8 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 27-32% PEG 3350, 0.05M Tris-sulfate, 3.5mM 2-mercaptoethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 11, 2007 |
Radiation | Monochromator: double-bounce downward / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→38.72 Å / Num. all: 27728 / Num. obs: 27728 / % possible obs: 97 % / Redundancy: 3.9 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 27.1 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2556 / % possible all: 90.3 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1LG6 Resolution: 1.7→38.72 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 85750.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.2781 Å2 / ksol: 0.378553 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.4 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→38.72 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.76 Å / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|