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Yorodumi- PDB-6qfv: Human carbonic anhydrase II with bound IrCp* complex (cofactor 8)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qfv | |||||||||||||||
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Title | Human carbonic anhydrase II with bound IrCp* complex (cofactor 8) 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: 1.45 Å | |||||||||||||||
Authors | Rebelein, J.G. | |||||||||||||||
Funding support | Switzerland, Germany, 4items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qfv.cif.gz | 74.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qfv.ent.gz | 53.4 KB | Display | PDB format |
PDBx/mmJSON format | 6qfv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/6qfv ftp://data.pdbj.org/pub/pdb/validation_reports/qf/6qfv | HTTPS FTP |
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-Related structure data
Related structure data | 6qfuC 6qfwC 6qfxC 3zp9S S: Starting model for refinement C: citing same article (ref.) |
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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: 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 | ||
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#2: Chemical | ChemComp-J0N / | ||
#3: Chemical | ChemComp-ZN / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.06 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 30, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→41.68 Å / Num. obs: 43249 / % possible obs: 96.7 % / Redundancy: 6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.45→1.47 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2208 / CC1/2: 0.488 / % possible all: 71.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZP9 Resolution: 1.45→41.1 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.97 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 64.09 Å2 / Biso mean: 17.442 Å2 / Biso min: 8.16 Å2
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Refinement step | Cycle: final / Resolution: 1.45→41.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Total num. of bins used: 20
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