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Yorodumi- PDB-8cdx: Human carbonic anhydrase I complexed with 4-(3-ethylureido)benzen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cdx | ||||||
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Title | Human carbonic anhydrase I complexed with 4-(3-ethylureido)benzenesulfonamide | ||||||
Components | Carbonic anhydrase 1 | ||||||
Keywords | LYASE / carbonic anhydrase I / sulfonamide / metalloenzyme / inhibitor | ||||||
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 / extracellular exosome / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.335 Å | ||||||
Authors | Angeli, A. / Ferraroni, M. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Human carbonic anhydrase I complexed with 4-(3-ethylureido)benzenesulfonamide Authors: Angeli, A. / Ferraroni, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cdx.cif.gz | 222 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cdx.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8cdx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/8cdx ftp://data.pdbj.org/pub/pdb/validation_reports/cd/8cdx | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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: Escherichia coli (E. coli) / References: UniProt: P00915, carbonic anhydrase #2: Chemical | #3: Chemical | Mass: 243.283 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N3O3S / Feature type: SUBJECT OF INVESTIGATION #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: 2.32 Å3/Da / Density % sol: 47.07 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 28-31% PEG4000, 0.2 M Sodium acetate, 0.1 M Tris pH 8.5-9.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9718 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 3, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9718 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→46.85 Å / Num. obs: 122663 / % possible obs: 99.9 % / Redundancy: 12 % / CC1/2: 0.999 / Rmerge(I) obs: 0.216 / Rrim(I) all: 0.225 / Net I/σ(I): 16.93 |
Reflection shell | Resolution: 1.33→1.37 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 2.34 / Num. unique obs: 8895 / CC1/2: 0.839 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.335→46.85 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.745 / SU ML: 0.032 / Cross valid method: NONE / ESU R: 0.048 / ESU R Free: 0.048 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.352 Å2
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Refinement step | Cycle: LAST / Resolution: 1.335→46.85 Å
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Refine LS restraints |
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LS refinement shell |
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