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Yorodumi- PDB-6qfu: Human carbonic anhydrase II with bound IrCp* complex (cofactor 7)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qfu | |||||||||||||||
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Title | Human carbonic anhydrase II with bound IrCp* complex (cofactor 7) 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 / 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 | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 | 6qfu.cif.gz | 71.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qfu.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 6qfu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qfu_validation.pdf.gz | 729.7 KB | Display | wwPDB validaton report |
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Full document | 6qfu_full_validation.pdf.gz | 730.9 KB | Display | |
Data in XML | 6qfu_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 6qfu_validation.cif.gz | 19.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/6qfu ftp://data.pdbj.org/pub/pdb/validation_reports/qf/6qfu | HTTPS FTP |
-Related structure data
Related structure data | 6qfvC 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-J0K / |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-SO4 / |
#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: 2.1 Å3/Da / Density % sol: 41.38 % / Description: Plates |
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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: Oct 31, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40.77 Å / Num. obs: 21112 / % possible obs: 99.3 % / Redundancy: 8 % / CC1/2: 0.958 / Rmerge(I) obs: 0.198 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 8.5 % / Rmerge(I) obs: 1.026 / Mean I/σ(I) obs: 7 / Num. unique obs: 1553 / CC1/2: 0.386 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZP9 Resolution: 1.8→40.77 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.112 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.47 Å2 / Biso mean: 17.635 Å2 / Biso min: 5.93 Å2
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Refinement step | Cycle: final / Resolution: 1.8→40.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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