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Yorodumi- PDB-3kon: Crystal structure of cobalt (II) human carbonic anhydrase II at p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kon | ||||||
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Title | Crystal structure of cobalt (II) human carbonic anhydrase II at pH 11.0 | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / Carbonic anhydrase / metalloenzyme / cobalt substitution / crystal pH | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Avvaru, B.S. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2010 Title: Comparison of solution and crystal properties of Co(II)-substituted human carbonic anhydrase II. Authors: Avvaru, B.S. / Arenas, D.J. / Tu, C. / Tanner, D.B. / McKenna, R. / Silverman, D.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kon.cif.gz | 69.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kon.ent.gz | 49.8 KB | Display | PDB format |
PDBx/mmJSON format | 3kon.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/3kon ftp://data.pdbj.org/pub/pdb/validation_reports/ko/3kon | HTTPS FTP |
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-Related 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: 29289.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P00918, carbonic anhydrase |
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#2: Chemical | ChemComp-CO / |
#3: 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: 2.08 Å3/Da / Density % sol: 40.97 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 11 Details: 1.4 M sodium citrate, pH 11.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 15, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 39055 / Num. obs: 38235 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.08 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 6 / Num. unique all: 3815 / Rsym value: 0.3 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→50 Å / Num. parameters: 9127 / Num. restraintsaints: 8589 / Cross valid method: FREE R / σ(F): 2 / σ(I): 2 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2260.2 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→50 Å
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Refine LS restraints |
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