+Open data
-Basic information
Entry | Database: PDB / ID: 3mnk | ||||||
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Title | Human Carbonic Anhydrase II Mutant K170H | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | PROTON TRANSPORT / proton transfer / metalloenzyme | ||||||
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: 1.75 Å | ||||||
Authors | Domsic, J.F. / McKenna, R. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Structural and kinetic study of the extended active site for proton transfer in human carbonic anhydrase II. Authors: Domsic, J.F. / Williams, W. / Fisher, S.Z. / Tu, C. / Agbandje-McKenna, M. / Silverman, D.N. / McKenna, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mnk.cif.gz | 67.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mnk.ent.gz | 48.6 KB | Display | PDB format |
PDBx/mmJSON format | 3mnk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mnk_validation.pdf.gz | 424.6 KB | Display | wwPDB validaton report |
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Full document | 3mnk_full_validation.pdf.gz | 425.1 KB | Display | |
Data in XML | 3mnk_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 3mnk_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mn/3mnk ftp://data.pdbj.org/pub/pdb/validation_reports/mn/3mnk | HTTPS FTP |
-Related structure data
Related structure data | 3mnhC 3mniC 3mnjC 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: 29298.027 Da / Num. of mol.: 1 / Mutation: K170H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P00918, carbonic anhydrase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-NA / |
#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: 2.13 Å3/Da / Density % sol: 42.37 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.3M Sodium Citrate, 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: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 1, 2008 |
Radiation | Monochromator: osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 23388 / % possible obs: 92.7 % / Redundancy: 3.2 % / Rsym value: 0.054 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 2025 / Rsym value: 0.323 / % possible all: 80.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TBT Resolution: 1.75→24.81 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.884 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.036 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→24.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.794 Å / Total num. of bins used: 20
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