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Yorodumi- PDB-5e2m: Crystal structure of human carbonic anhydrase isozyme I with 3-(c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e2m | ||||||
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Title | Crystal structure of human carbonic anhydrase isozyme I with 3-(cyclooctylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide | ||||||
Components | Carbonic anhydrase 1 | ||||||
Keywords | LYASE / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / lyase-lyase inhibitor complex | ||||||
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 / molecular replacement / Resolution: 1.41 Å | ||||||
Authors | Manakova, E. / Smirnov, A. / Grazulis, S. | ||||||
Citation | Journal: ChemMedChem / Year: 2017 Title: Intrinsic Thermodynamics and Structures of 2,4- and 3,4-Substituted Fluorinated Benzenesulfonamides Binding to Carbonic Anhydrases. Authors: Zubriene, A. / Smirnov, A. / Dudutiene, V. / Timm, D.D. / Matuliene, J. / Michailoviene, V. / Zaksauskas, A. / Manakova, E. / Grazulis, S. / Matulis, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e2m.cif.gz | 132.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e2m.ent.gz | 101.1 KB | Display | PDB format |
PDBx/mmJSON format | 5e2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/5e2m ftp://data.pdbj.org/pub/pdb/validation_reports/e2/5e2m | HTTPS FTP |
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-Related structure data
Related structure data | 5dogC 5dohC 5drsC 5e2nC 5eheC 2cabS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 28835.105 Da / Num. of mol.: 2 / Fragment: human carbonic anhydrase I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00915, carbonic anhydrase |
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-Non-polymers , 5 types, 542 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 2.26 Å3/Da / Density % sol: 45.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.4 Details: Crystallization buffer contains 0.1M TrisHCl (pH 8.5), 0.2M ammonium acetate, 28% of PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.826606 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.826606 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.41→119.722 Å / Num. all: 103444 / Num. obs: 103444 / % possible obs: 98 % / Redundancy: 12.8 % / Biso Wilson estimate: 17.854 Å2 / Rpim(I) all: 0.011 / Rrim(I) all: 0.04 / Rsym value: 0.035 / Net I/av σ(I): 7.292 / Net I/σ(I): 34.4 / Num. measured all: 1326865 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CAB Resolution: 1.41→61.52 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.19 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.859 / SU R Cruickshank DPI: 0.068 / SU Rfree: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108.98 Å2 / Biso mean: 21.131 Å2 / Biso min: 8.94 Å2
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Refinement step | Cycle: LAST / Resolution: 1.41→61.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.41→1.447 Å / Total num. of bins used: 20
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