+Open data
-Basic information
Entry | Database: PDB / ID: 6mbv | ||||||
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Title | Carbonic Anhydrase II in complex with Nicotinic Acid | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / carbonic anhydrase II / carboxylic acid / nicotinic acid | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.695 Å | ||||||
Authors | Lomelino, C.L. / McKenna, R. | ||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2019 Title: Carbonic anhydrase II in complex with carboxylic acid-based inhibitors. Authors: Lomelino, C.L. / McKenna, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mbv.cif.gz | 163.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mbv.ent.gz | 128.5 KB | Display | PDB format |
PDBx/mmJSON format | 6mbv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mb/6mbv ftp://data.pdbj.org/pub/pdb/validation_reports/mb/6mbv | HTTPS FTP |
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-Related structure data
Related structure data | 6mbyC 3ks3S S: Starting model for refinement 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: 28932.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-NIO / |
#4: Chemical | ChemComp-GOL / |
#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: 2.08 Å3/Da / Density % sol: 40.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6 M NaCitrate, 50 mM Tris |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.977 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 16, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.69→31.91 Å / Num. obs: 26067 / % possible obs: 97.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 16.62 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.038 / Rrim(I) all: 0.072 / Net I/σ(I): 13.7 / Num. measured all: 88423 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KS3 Resolution: 1.695→31.912 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.27 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.54 Å2 / Biso mean: 23.2248 Å2 / Biso min: 8.51 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.695→31.912 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Origin x: -30.5533 Å / Origin y: -1.8585 Å / Origin z: 15.8622 Å
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Refinement TLS group |
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