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Yorodumi- PDB-1tbt: Effect of Shuttle Location and pH Environment on H+ Transfer in H... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tbt | ||||||
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Title | Effect of Shuttle Location and pH Environment on H+ Transfer in Human Carbonic Anhydrase II | ||||||
Components | Carbonic anhydrase II | ||||||
Keywords | LYASE / proton shuttle carbonic anhydrase metalloenzyme | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Fisher, Z. / Hernandez Prada, J.A. / Tu, C.K. / Duda, D. / Yoshioka, C. / An, H. / Govindasamy, L. / Silverman, D.N. / McKenna, R. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Structural and Kinetic Characterization of Active-Site Histidine as a Proton Shuttle in Catalysis by Human Carbonic Anhydrase II. Authors: Fisher, Z. / Hernandez Prada, J.A. / Tu, C. / Duda, D. / Yoshioka, C. / An, H. / Govindasamy, L. / 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 | 1tbt.cif.gz | 67.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tbt.ent.gz | 48.8 KB | Display | PDB format |
PDBx/mmJSON format | 1tbt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tbt_validation.pdf.gz | 422.3 KB | Display | wwPDB validaton report |
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Full document | 1tbt_full_validation.pdf.gz | 423.2 KB | Display | |
Data in XML | 1tbt_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 1tbt_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tb/1tbt ftp://data.pdbj.org/pub/pdb/validation_reports/tb/1tbt | HTTPS FTP |
-Related structure data
Related structure data | 1t9nC 1tb0C 1te3C 1teqC 1teuC 1tg3C 1tg9C 1th9C 1thkC 2cbaS C: citing same article (ref.) 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: pET31 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / 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: 2.13 Å3/Da / Density % sol: 42.31 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 50 mM Tris-Cl pH7.0, 2.5 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: Osmic mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 15878 / Rsym value: 0.051 |
Reflection shell | Resolution: 2→2.07 Å / Num. unique all: 15878 / Rsym value: 0.14 / % possible all: 91.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2CBA Resolution: 2→20 Å / Rfactor Rfree: 0.184 / Rfactor Rwork: 0.13 / Cross valid method: Random / Stereochemistry target values: Engh & Huber | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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