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Yorodumi- PDB-3p3h: Human carbonic anhydrase II in complex with p-(5-ferrocenyl-1H-1,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p3h | ||||||
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Title | Human carbonic anhydrase II in complex with p-(5-ferrocenyl-1H-1,2,3-triazol-1-yl)benzenesulfonamide | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / carbonic anhydrase alpha / cytosolic | ||||||
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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å | ||||||
Authors | Salmon, A.J. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2012 Title: Protein crystal structures with ferrocene and ruthenocene-based enzyme inhibitors. Authors: Salmon, A.J. / Williams, M.L. / Hofmann, A. / Poulsen, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p3h.cif.gz | 122.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p3h.ent.gz | 92.2 KB | Display | PDB format |
PDBx/mmJSON format | 3p3h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p3/3p3h ftp://data.pdbj.org/pub/pdb/validation_reports/p3/3p3h | HTTPS FTP |
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-Related structure data
Related structure data | 3p3jC 3p44C 3p55C 3hknS 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: pET8c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00918, carbonic anhydrase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-84A / |
#4: Chemical | ChemComp-GOL / |
#5: 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: 41.54 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 2.6M ammonium sulfate, 0.1M glycine, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.957 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 8, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.957 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→22.92 Å / Num. obs: 39283 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Redundancy: 4 % / Biso Wilson estimate: 11.3 Å2 / Rsym value: 0.059 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 3.9 % / Num. unique all: 2700 / Rsym value: 0.174 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3HKN Resolution: 1.5→22.92 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.07 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R Free: 0.079 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.12 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→22.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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