+Open data
-Basic information
Entry | Database: PDB / ID: 6swm | ||||||
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Title | selenol bound carbonic anhydrase I | ||||||
Components | Carbonic anhydrase 1 | ||||||
Keywords | LYASE / carbonic anhydrase / inhibitor / selenol | ||||||
Function / homology | Function and homology information hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen ...hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / one-carbon metabolic process / zinc ion binding / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.77 Å | ||||||
Authors | Angeli, A. / Ferraroni, M. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2019 Title: Selenols: a new class of carbonic anhydrase inhibitors. Authors: Angeli, A. / Tanini, D. / Nocentini, A. / Capperucci, A. / Ferraroni, M. / Gratteri, P. / Supuran, C.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6swm.cif.gz | 114.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6swm.ent.gz | 87.8 KB | Display | PDB format |
PDBx/mmJSON format | 6swm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6swm_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6swm_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6swm_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 6swm_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sw/6swm ftp://data.pdbj.org/pub/pdb/validation_reports/sw/6swm | HTTPS FTP |
-Related structure data
Related structure data | 6hwzC 6hx5C 3lxeS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28906.186 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA1 / Production host: Homo sapiens (human) / References: UniProt: P00915, carbonic anhydrase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.33 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 28-31% PEG4000, 0.2 M Sodium acetate, 0.1 M Tris pH 8.5-9.0 PH range: 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.54184 Å |
Detector | Type: Bruker PHOTON III / Detector: PIXEL / Date: Aug 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→46.66 Å / Num. obs: 13857 / % possible obs: 97.1 % / Redundancy: 4.2 % / CC1/2: 0.977 / Rrim(I) all: 0.25 / Net I/σ(I): 6.19 |
Reflection shell | Resolution: 2.75→2.91 Å / Num. unique obs: 2172 / CC1/2: 0.336 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LXE Resolution: 2.77→46.66 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.828 / SU B: 30.111 / SU ML: 0.522 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.529 / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 112.98 Å2 / Biso mean: 46.333 Å2 / Biso min: 0.5 Å2
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Refinement step | Cycle: final / Resolution: 2.77→46.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.77→2.839 Å / Rfactor Rfree error: 0
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