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Yorodumi- PDB-5ll9: Crystal structure of human carbonic anhydrase isozyme XII with 4-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ll9 | ||||||
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Title | Crystal structure of human carbonic anhydrase isozyme XII with 4-(1H-benzimidazol-1-ylacetyl)-2-chlorobenzenesulfonamide | ||||||
Components | Carbonic anhydrase 12 | ||||||
Keywords | LYASE / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / lyase-lyase inhibitor comple | ||||||
Function / homology | Function and homology information chloride ion homeostasis / estrous cycle / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / basolateral plasma membrane / apical plasma membrane / zinc ion binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å | ||||||
Authors | Smirnov, A. / Manakova, E. / Grazulis, S. | ||||||
Citation | Journal: Chemistryselect / Year: 2017 Title: Combinatorial Design of Isoform-Selective N-Alkylated Benzimidazole-Based Inhibitors of Carbonic Anhydrases Authors: Capkauskaite, E. / Linkuviene, V. / Smirnov, A. / Milinaviciute, G. / Timm, D. / Kasiliauskaite, 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 | 5ll9.cif.gz | 255.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ll9.ent.gz | 203.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ll9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ll9_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 5ll9_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5ll9_validation.xml.gz | 53.8 KB | Display | |
Data in CIF | 5ll9_validation.cif.gz | 80.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ll/5ll9 ftp://data.pdbj.org/pub/pdb/validation_reports/ll/5ll9 | HTTPS FTP |
-Related structure data
Related structure data | 5ll4C 5ll5C 5llaC 1jd0S 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 29917.318 Da / Num. of mol.: 4 / Fragment: human carbonic anhydrase XII Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA12 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: O43570, carbonic anhydrase |
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-Non-polymers , 5 types, 1233 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-6YQ / #4: Chemical | ChemComp-EDO / #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: 2.06 Å3/Da / Density % sol: 39.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Crystallization buffer: 0.1M ammonium citrate (pH 7), 0.2M ammonium sulfate and 30% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.826606 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.826606 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.45→86.436 Å / Num. all: 170401 / Num. obs: 170401 / % possible obs: 99.1 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.02 / Rrim(I) all: 0.054 / Rsym value: 0.045 / Net I/av σ(I): 11.35 / Net I/σ(I): 21.8 / Num. measured all: 1174019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1JD0 Resolution: 1.45→73.19 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU R Cruickshank DPI: 0.0763 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.078 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: 69.14 Å2 / Biso mean: 17.177 Å2 / Biso min: 5.63 Å2
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Refinement step | Cycle: final / Resolution: 1.45→73.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Total num. of bins used: 20
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