[English] 日本語
Yorodumi- PDB-4y0j: H/D exchanged human carbonic anhydrase II pH 6 room temperature n... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4y0j | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | H/D exchanged human carbonic anhydrase II pH 6 room temperature neutron crystal structure. | |||||||||
Components | Carbonic anhydrase 2 | |||||||||
Keywords | LYASE / neutron / proton transfer / H/D exchanged | |||||||||
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 / 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 / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Fisher, S.Z. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Joint neutron crystallographic and NMR solution studies of Tyr residue ionization and hydrogen bonding: Implications for enzyme-mediated proton transfer. Authors: Michalczyk, R. / Unkefer, C.J. / Bacik, J.P. / Schrader, T.E. / Ostermann, A. / Kovalevsky, A.Y. / McKenna, R. / Fisher, S.Z. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4y0j.cif.gz | 119 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4y0j.ent.gz | 93 KB | Display | PDB format |
PDBx/mmJSON format | 4y0j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/4y0j ftp://data.pdbj.org/pub/pdb/validation_reports/y0/4y0j | HTTPS FTP |
---|
-Related structure data
Related structure data | 4q49C 1tbtS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 29070.785 Da / Num. of mol.: 1 / Fragment: UNP residues 3-260 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00918, carbonic anhydrase |
---|---|
#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-DOD / |
-Experimental details
-Experiment
Experiment | Method: NEUTRON DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.13 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Large drops 500 microliters in 9-well glass plate in sandwich box set-up. Crystals took 3 months to grow to maximal size. Temp details: ambient |
-Data collection
Diffraction | Mean temperature: 293 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: NUCLEAR REACTOR / Site: LANSCE / Beamline: PCS / Wavelength: 0.7 - 6.5 | |||||||||
Detector | Type: 3He-position sensitive detector. / Detector: CCD / Date: Nov 1, 2012 | |||||||||
Radiation | Monochromator: None / Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 2→20 Å / Num. obs: 13799 / % possible obs: 82 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.228 / Net I/σ(I): 4.5 | |||||||||
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 1.5 / % possible all: 70 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1tbt Resolution: 2→20 Å / Cross valid method: FREE R-VALUE
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
|