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Yorodumi- PDB-4hba: Structural and Catalytic Characterization of a Thermal and Acid S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hba | ||||||
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Title | Structural and Catalytic Characterization of a Thermal and Acid Stable Variant of Human Carbonic Anhydrase II Containing an Engineered Disulfide Bond | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / human carbonic anhydrase II / thermal stability | ||||||
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: 1.762 Å | ||||||
Authors | Boone, C.D. / Habibzadegan, A. / McKenna, R. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structural and catalytic characterization of a thermally stable and acid-stable variant of human carbonic anhydrase II containing an engineered disulfide bond. Authors: Boone, C.D. / Habibzadegan, A. / Tu, C. / Silverman, D.N. / McKenna, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hba.cif.gz | 166.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hba.ent.gz | 140 KB | Display | PDB format |
PDBx/mmJSON format | 4hba.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/4hba ftp://data.pdbj.org/pub/pdb/validation_reports/hb/4hba | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29295.047 Da / Num. of mol.: 1 / Mutation: A23C, L203C, C206S 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-ZN / | ||
#3: Chemical | #4: 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: 2.06 Å3/Da / Density % sol: 40.36 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 9 Details: 1.3M sodium citrate, 50mM Tris-HCl, pH 9.0, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 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 4, 2012 |
Radiation | Monochromator: Varimax Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→20 Å / Num. all: 23734 / Num. obs: 23307 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 1.77→1.83 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.5 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.762→19.914 Å / Occupancy max: 1 / Occupancy min: 0.26 / FOM work R set: 0.8844 / SU ML: 0.19 / σ(F): 1.34 / Phase error: 18.5 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.48 Å2 / Biso mean: 21.0162 Å2 / Biso min: 8.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.762→19.914 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Refinement TLS params. | Method: refined / Origin x: -5.8257 Å / Origin y: -1.8945 Å / Origin z: 85.0602 Å
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Refinement TLS group |
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