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Yorodumi- PDB-2ax2: Production and X-ray crystallographic analysis of fully deuterate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ax2 | ||||||
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Title | Production and X-ray crystallographic analysis of fully deuterated human carbonic anhydrase II | ||||||
Components | Carbonic anhydrase II | ||||||
Keywords | LYASE / perdeurated human carbonic anhydrase II proton transfer | ||||||
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: 1.5 Å | ||||||
Authors | Budayova-Spano, M. / Fisher, S.Z. / Dauvergne, M.T. / Silverman, D.N. / Myles, D.A.A. / McKenna, R.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2006 Title: Production and X-ray crystallographic analysis of fully deuterated human carbonic anhydrase II. Authors: Budayova-Spano, M. / Fisher, S.Z. / Dauvergne, M.T. / Agbandje-McKenna, M. / Silverman, D.N. / Myles, D.A. / McKenna, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ax2.cif.gz | 69.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ax2.ent.gz | 49.9 KB | Display | PDB format |
PDBx/mmJSON format | 2ax2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ax2_validation.pdf.gz | 430.5 KB | Display | wwPDB validaton report |
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Full document | 2ax2_full_validation.pdf.gz | 435.2 KB | Display | |
Data in XML | 2ax2_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 2ax2_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/2ax2 ftp://data.pdbj.org/pub/pdb/validation_reports/ax/2ax2 | HTTPS FTP |
-Related structure data
Related structure data | 1tbtS S: Starting model for refinement |
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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: 29289.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00918, carbonic anhydrase |
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#2: Chemical | ChemComp-ZN / |
#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: 2.1 Å3/Da / Density % sol: 40.9 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.15 M sodium citrate, 100 mM Tris-Dl, pH7.8, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.00522 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 8, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00522 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. obs: 37372 / % possible obs: 97 % / Redundancy: 3 % |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 2.3 % / Num. unique all: 3689 / Rsym value: 0.17 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1TBT Resolution: 1.5→20 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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Refine LS restraints |
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