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Yorodumi- PDB-1ugf: HUMAN CARBONIC ANHYDRASE II [HCAII] (E.C.4.2.1.1) MUTANT WITH ALA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ugf | ||||||
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Title | HUMAN CARBONIC ANHYDRASE II [HCAII] (E.C.4.2.1.1) MUTANT WITH ALA 65 REPLACED BY THR (A65T) | ||||||
Components | CARBONIC ANHYDRASE II | ||||||
Keywords | LYASE / ACETYLATION / ZINC / POLYMORPHISM / DISEASE MUTATION | ||||||
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 / DIFFERENCE FOURIER / Resolution: 2 Å | ||||||
Authors | Scolnick, L.R. / Christianson, D.W. | ||||||
Citation | Journal: Biochemistry / Year: 1996 Title: X-ray crystallographic studies of alanine-65 variants of carbonic anhydrase II reveal the structural basis of compromised proton transfer in catalysis. Authors: Scolnick, L.R. / Christianson, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ugf.cif.gz | 67 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ugf.ent.gz | 48 KB | Display | PDB format |
PDBx/mmJSON format | 1ugf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ugf_validation.pdf.gz | 368 KB | Display | wwPDB validaton report |
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Full document | 1ugf_full_validation.pdf.gz | 369.3 KB | Display | |
Data in XML | 1ugf_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 1ugf_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ug/1ugf ftp://data.pdbj.org/pub/pdb/validation_reports/ug/1ugf | HTTPS FTP |
-Related structure data
Related structure data | 1ugaC 1ugbC 1ugcC 1ugdC 1ugeC 1uggC C: citing same article (ref.) |
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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: 29100.812 Da / Num. of mol.: 1 / Mutation: A65T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Gene: CAII / Plasmid: PCAM / Species (production host): Escherichia coli / Gene (production host): CAII / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P00918, carbonic anhydrase |
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#2: Chemical | ChemComp-HG / |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-AZI / |
#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: 2.17 Å3/Da / Density % sol: 44 % | ||||||||||||||||||||
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Crystal grow | pH: 8 / Details: 50MM TRIS-HCL, PH=8.0, 1.95 - 3.9M NH4SO4 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jan 15, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→7.2 Å / Num. obs: 17315 / % possible obs: 94.7 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 16.2 Å2 / Rsym value: 0.059 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.16 / % possible all: 74.6 |
Reflection | *PLUS Num. measured all: 41320 / Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS % possible obs: 74.6 % / Rmerge(I) obs: 0.16 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: NATIVE CAII, (HAKANSSON, ET AL., 1992) Resolution: 2→6.5 Å / Cross valid method: R-FREE / σ(F): 2
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Displacement parameters | Biso mean: 17.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 12 Å / Luzzati sigma a obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→6.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.24 |