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Yorodumi- PDB-4qiz: Crystal structure of human carbonic anhydrase isozyme XIII with i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qiz | ||||||
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Title | Crystal structure of human carbonic anhydrase isozyme XIII with inhibitor | ||||||
Components | Carbonic anhydrase 13 | ||||||
Keywords | LYASE/LYASE INHIBITOR / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å | ||||||
Authors | Manakova, E. / Smirnov, A. / Grazulis, S. | ||||||
Citation | Journal: Chemmedchem / Year: 2015 Title: Functionalization of Fluorinated Benzenesulfonamides and Their Inhibitory Properties toward Carbonic Anhydrases Authors: Dudutiene, V. / Zubriene, A. / Smirnov, A. / Timm, D.D. / Smirnoviene, J. / Kazokaite, 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 | 4qiz.cif.gz | 132.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qiz.ent.gz | 102.4 KB | Display | PDB format |
PDBx/mmJSON format | 4qiz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qiz_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4qiz_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4qiz_validation.xml.gz | 29.5 KB | Display | |
Data in CIF | 4qiz_validation.cif.gz | 42 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/4qiz ftp://data.pdbj.org/pub/pdb/validation_reports/qi/4qiz | HTTPS FTP |
-Related structure data
Related structure data | 4qiyC 4qj0C 4qjmC 4qjoC 4qjpC 4qjwC 4qjxC 4qtlC 2nnoS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29613.318 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA13 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8N1Q1, carbonic anhydrase #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 43.49 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1M ammonium citrate (pH 5.0), 20% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-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: Dec 2, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: High Heat Load (HHL) Monochromator: Si 111; Large Offset Monochromator (LOM): Si 311, Si 511 Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.826606 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→57.1 Å / Num. obs: 75960 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rsym value: 0.037 / Net I/σ(I): 27.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2NNO Resolution: 1.55→46.16 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 mean: 19.49 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→46.16 Å
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Refine LS restraints |
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