[English] 日本語
Yorodumi- PDB-6qfw: Human carbonic anhydrase II with bound IrCp* complex (cofactor 9)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qfw | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Human carbonic anhydrase II with bound IrCp* complex (cofactor 9) to generate an artificial transfer hydrogenase (ATHase) | |||||||||||||||
Components | Carbonic anhydrase 2 | |||||||||||||||
Keywords | OXIDOREDUCTASE / Artificial Transfer Hydrogenase / bound IrCp* complex / zinc binding protein / human carbonic anhydrase II | |||||||||||||||
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: 1.2 Å | |||||||||||||||
Authors | Rebelein, J.G. | |||||||||||||||
Funding support | Switzerland, Germany, 4items
| |||||||||||||||
Citation | Journal: Acs Catalysis / Year: 2019 Title: Chemical Optimization of Whole-Cell Transfer Hydrogenation Using Carbonic Anhydrase as Host Protein. Authors: Rebelein, J.G. / Cotelle, Y. / Garabedian, B. / Ward, T.R. | |||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6qfw.cif.gz | 76.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6qfw.ent.gz | 54.7 KB | Display | PDB format |
PDBx/mmJSON format | 6qfw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/6qfw ftp://data.pdbj.org/pub/pdb/validation_reports/qf/6qfw | HTTPS FTP |
---|
-Related structure data
Related structure data | 6qfuC 6qfvC 6qfxC 3zp9S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29273.062 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 |
---|
-Non-polymers , 5 types, 271 molecules
#2: Chemical | ChemComp-JR8 / |
---|---|
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-IR / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.26 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.9 / Details: 2.6 M ammonium sulfate, 50 mM Tris-H2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→40.95 Å / Num. obs: 70789 / % possible obs: 98 % / Redundancy: 9.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.134 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.2→1.23 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 7 / Num. unique obs: 5020 / CC1/2: 0.975 / % possible all: 94.4 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZP9 Resolution: 1.2→40.95 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 132.48 Å2 / Biso mean: 14.7 Å2 / Biso min: 5.77 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.2→40.95 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.2→1.231 Å / Total num. of bins used: 20
|