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Yorodumi- PDB-5ogj: Crystal structure of human carbonic anhydrase isozyme XIII with 2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ogj | ||||||
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Title | Crystal structure of human carbonic anhydrase isozyme XIII with 2-(Cyclooctylamino)-3,5,6-trifluoro-4-[(2-hydroxyethyl)thio]benzenesulfonamide | ||||||
Components | Carbonic anhydrase 13 | ||||||
Keywords | LYASE / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / lyase-lyase inhibitor complex | ||||||
Function / homology | Function and homology information Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / myelin sheath / intracellular membrane-bounded organelle / zinc ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.06 Å | ||||||
Authors | Manakova, E. / Smirnov, A. / Grazulis, S. | ||||||
Citation | Journal: To be published Title: Crystal structure of human carbonic anhydrase isozyme XIII with 2-(Cyclooctylamino)-3,5,6-trifluoro-4-[(2-hydroxyethyl)thio]benzenesulfonamide Authors: Smirnov, 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 | 5ogj.cif.gz | 265 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ogj.ent.gz | 212.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ogj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/5ogj ftp://data.pdbj.org/pub/pdb/validation_reports/og/5ogj | HTTPS FTP |
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-Related structure data
Related structure data | 4hu1S 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 BA
#1: Protein | Mass: 29613.318 Da / Num. of mol.: 2 / Fragment: human carbonic anhydrase XIII Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA13 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8N1Q1, carbonic anhydrase |
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-Non-polymers , 7 types, 730 molecules
#2: Chemical | #3: Chemical | ChemComp-CIT / #4: Chemical | ChemComp-PEG / | #5: Chemical | #6: Chemical | ChemComp-EDO / #7: Chemical | #8: 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: 2.18 Å3/Da / Density % sol: 43.56 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 291 K / Method: evaporation / pH: 5 Details: Crystallization buffer: 0.1M ammonium citrate (pH 7), 0.1M sodium acetate (pH 4.5) and 26% PEG3350 |
-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: 0.9763 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.06→79.891 Å / Num. obs: 229112 / % possible obs: 98.6 % / Redundancy: 6 % / Rpim(I) all: 0.021 / Rrim(I) all: 0.052 / Rsym value: 0.042 / Net I/av σ(I): 6.26 / Net I/σ(I): 18.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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: 4HU1 Resolution: 1.06→79.89 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU R Cruickshank DPI: 0.0263 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.027 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 146.86 Å2 / Biso mean: 15.406 Å2 / Biso min: 5.48 Å2
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Refinement step | Cycle: final / Resolution: 1.06→79.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.063→1.091 Å / Total num. of bins used: 20
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