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Yorodumi- PDB-4fik: Human carbonic anhydrase II H64A complexed with thioxolone hydrol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fik | |||||||||
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Title | Human carbonic anhydrase II H64A complexed with thioxolone hydrolysis products | |||||||||
Components | Carbonic anhydrase 2 | |||||||||
Keywords | LYASE / CARBONIC ANHYDRASE II / HUMAN CARBONIC ANHYDRASE II / HCA II / HCA2 / CA II / CA2 / CARBONATE DEHYDRATASE II / CARBONIC ANHYDRASE C / THIOXOLONE / 4-MERCAPTOBENZENE-1 / 3-DIOL / 4-(2 / 4-DIHYDROXYPHENYL) DISULFANYLBENZENE-1 / DISEASE MUTATION / METAL-BINDING | |||||||||
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 / SYNCHROTRON / AB INITIO / Resolution: 1.2 Å | |||||||||
Authors | Sippel, K.H. / Genis, C. / Govindasamy, L. / Agbandje-McKenna, M. / Tripp, B.C. / McKenna, R. | |||||||||
Citation | Journal: J Phys Chem Lett / Year: 2010 Title: Synchrotron Radiation Provides a Plausible Explanation for the Generation of a Free Radical Adduct of Thioxolone in Mutant Carbonic Anhydrase II. Authors: Sippel, K.H. / Genis, C. / Govindasamy, L. / Agbandje-McKenna, M. / Kiddle, J.J. / Tripp, B.C. / McKenna, R. #1: Journal: Biochemistry / Year: 2008 Title: Inhibition of Carbonic Anhydrase II by Thioxolone: A Mechanistic and Structural Study Authors: Barrese, A.A. / Genis, C. / Fisher, S.Z. / Orwenyo, J.N. / Kumara, M.T. / Dutta, S.K. / Phillips, E. / Kiddle, J.J. / Tu, C. / Silverman, D.N. / Govindasamy, L. / Agbandje-McKenna, M. / McKenna, R. / Tripp, B.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fik.cif.gz | 138.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fik.ent.gz | 106 KB | Display | PDB format |
PDBx/mmJSON format | 4fik.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/4fik ftp://data.pdbj.org/pub/pdb/validation_reports/fi/4fik | HTTPS FTP |
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-Related structure data
Related structure data | 1g0fS 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: 29221.992 Da / Num. of mol.: 1 / Mutation: H64A 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(DE3)PLYSS / References: UniProt: P00918, carbonic anhydrase |
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-Non-polymers , 7 types, 306 molecules
#2: Chemical | ChemComp-ZN / | ||||||||
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#3: Chemical | ChemComp-TH7 / | ||||||||
#4: Chemical | #5: Chemical | ChemComp-D2S / | #6: Chemical | ChemComp-GOL / | #7: Chemical | ChemComp-SO4 / | #8: 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: 41.33 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 50MM TRIS-HCL, 2.6M AMMONIUM SULFATE, 2UL OF 100UM THIOXOLONE ADDED TO DROP 24HRS PRIOR TO FREEZING, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.938 / Wavelength: 0.938 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 16, 2006 / Details: MIRRORS |
Radiation | Monochromator: HORIZONTAL BENT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.938 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→19.96 Å / Num. all: 75775 / Num. obs: 70016 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 8.36 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 2.7 / % possible all: 78.2 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO Starting model: PDB ENTRY 1G0F Resolution: 1.2→15.643 Å / SU ML: 0.08 Isotropic thermal model: Anisotropic for all full occupancy atoms Cross valid method: THROUGHOUT / σ(F): 0.03 / σ(I): 0 / Phase error: 11.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.6 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.7 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→15.643 Å
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Refine LS restraints |
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LS refinement shell |
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