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Yorodumi- PDB-3pyk: Human Carbonic Anhydrase II as Host for Pianostool Complexes Bear... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pyk | ||||||
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Title | Human Carbonic Anhydrase II as Host for Pianostool Complexes Bearing a Sulfonamide Anchor | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE/LYASE INHIBITOR / 10 STRANDED / TWISTED BETA-SHEETS / carbonate dehydratase activity / protein binding / zinc ion binding / lyase activity / metal ion binding / CO2 / bicarbonate / sulfonamides / metal ions / LYASE-LYASE INHIBITOR complex | ||||||
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 / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Heinisch, T. / Schirmer, T. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2011 Title: Human Carbonic Anhydrase II as a host for piano-stool complexes bearing a sulfonamide anchor. Authors: Monnard, F.W. / Heinisch, T. / Nogueira, E.S. / Schirmer, T. / 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 | 3pyk.cif.gz | 143.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pyk.ent.gz | 110.2 KB | Display | PDB format |
PDBx/mmJSON format | 3pyk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/3pyk ftp://data.pdbj.org/pub/pdb/validation_reports/py/3pyk | HTTPS FTP |
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-Related structure data
Related structure data | 2cbaS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29273.062 Da / Num. of mol.: 1 / Mutation: S2A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P00918, carbonic anhydrase |
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-Non-polymers , 5 types, 424 molecules
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-SRX / |
#4: Chemical | ChemComp-MMC / |
#5: Chemical | ChemComp-SO4 / |
#6: 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: 2.09 Å3/Da / Density % sol: 41.24 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 3 uL protein solution (20 mg/mL lyophilized hCAII in 50 mM Tris-sulfate, 1 mM methyl mercuric acetate) and 5 uL precipitating buffer (2.6 M ammonium sulfate, 50 mM Tris-sulfate were mixed ...Details: 3 uL protein solution (20 mg/mL lyophilized hCAII in 50 mM Tris-sulfate, 1 mM methyl mercuric acetate) and 5 uL precipitating buffer (2.6 M ammonium sulfate, 50 mM Tris-sulfate were mixed and equilibrated against 500 uL precipitating buffer. Single crystals were transferred into a cross-linking buffer, which was prepared from 10 uL precipitating buffer and 5 uL glutaraldehyde solution (0.8 % glutaraldehyde, 4 M ammonium sulfate, 50 mM Tris-sulfate) and equilibrated for 18 h. Cross-linked crystals were transferred into soaking buffer (9 uL precipitating buffer, 0.5 uL 60 mM {(6-benzene)Ru(bispy 3)Cl}+ in DMSO) and equilibrated for 54 h, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: OTHER / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 14, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→30.6 Å / Num. obs: 59007 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.3→1.334 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 2.8 / % possible all: 91.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2cba Resolution: 1.3→30.6 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.461 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.373 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→30.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 11.76 Å / Origin y: -1.003 Å / Origin z: 16.314 Å
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