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Yorodumi- PDB-3rld: Crystal structure of the Y7I mutant of human carbonic anhydrase II -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rld | ||||||
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Title | Crystal structure of the Y7I mutant of human carbonic anhydrase II | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / zinc metalloenzyme / histidine ligands / Y7I 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 / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Avvaru, B.S. / Mikulski, R. / McKenna, R. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2011 Title: Kinetic and crystallographic studies of the role of tyrosine 7 in the active site of human carbonic anhydrase II. Authors: Mikulski, R. / Avvaru, B.S. / Tu, C. / Case, N. / McKenna, R. / Silverman, D.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rld.cif.gz | 70.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rld.ent.gz | 49.7 KB | Display | PDB format |
PDBx/mmJSON format | 3rld.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rld_validation.pdf.gz | 439.9 KB | Display | wwPDB validaton report |
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Full document | 3rld_full_validation.pdf.gz | 441.6 KB | Display | |
Data in XML | 3rld_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 3rld_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rl/3rld ftp://data.pdbj.org/pub/pdb/validation_reports/rl/3rld | HTTPS FTP |
-Related structure data
Related structure data | 2iliS 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: 29239.047 Da / Num. of mol.: 1 / Mutation: Y7I 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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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | #4: 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: 2.15 Å3/Da / Density % sol: 42.89 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.7 M sodium citrate, 100 mM Tris, droplet is 1:1 mixture of the protein and reservoir, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 5, 2008 / Details: mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Osmic optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→20 Å / Num. all: 38853 / Num. obs: 36906 / % possible obs: 96.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.099 / Χ2: 4.934 / Net I/σ(I): 10.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2ili Resolution: 1.5→20 Å / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 99.67 Å2 / Biso mean: 21.0801 Å2 / Biso min: 9.07 Å2 | ||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.17 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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