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Yorodumi- PDB-2nxs: Structural and kinetic effects of hydrophobic mutations in the ac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nxs | ||||||
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Title | Structural and kinetic effects of hydrophobic mutations in the active site of human carbonic anhydrase II | ||||||
Components | carbonic anhydrase 2 | ||||||
Keywords | LYASE / proton transfer / histidine 64 / carbonic anhydrase | ||||||
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: 1.8 Å | ||||||
Authors | Fisher, S.Z. / McKenna, R. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Speeding Up Proton Transfer in a Fast Enzyme: Kinetic and Crystallographic Studies on the Effect of Hydrophobic Amino Acid Substitutions in the Active Site of Human Carbonic Anhydrase II. Authors: Fisher, S.Z. / Tu, C.K. / Bhatt, D. / Govindasamy, L. / Agbandje-McKenna, M. / 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 | 2nxs.cif.gz | 67 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nxs.ent.gz | 47.9 KB | Display | PDB format |
PDBx/mmJSON format | 2nxs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nxs_validation.pdf.gz | 438.1 KB | Display | wwPDB validaton report |
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Full document | 2nxs_full_validation.pdf.gz | 441.9 KB | Display | |
Data in XML | 2nxs_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 2nxs_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/2nxs ftp://data.pdbj.org/pub/pdb/validation_reports/nx/2nxs | HTTPS FTP |
-Related structure data
Related structure data | 2nwoC 2nwpC 2nwyC 2nwzC 2nxrC 2nxtC 1tbtS 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: 29273.062 Da / Num. of mol.: 1 / Mutation: Y7F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00918, carbonic anhydrase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-SO4 / |
#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: 42.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10 Details: 50 mM Tris-Cl pH 10, 2.6 M ammonium sulfate, pH 10.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 6, 2006 / Details: osmic mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 20874 / % possible obs: 89.4 % / Observed criterion σ(I): 18.1 / Redundancy: 3.1 % / Rsym value: 0.071 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.2 % / Num. unique all: 1951 / Rsym value: 0.238 / % possible all: 83.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1tbt Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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