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Yorodumi- PDB-4hu1: Crystal structure of human carbonic anhydrase isozyme XIII with t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hu1 | ||||||
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Title | Crystal structure of human carbonic anhydrase isozyme XIII with the inhibitor. | ||||||
Components | Carbonic anhydrase 13 | ||||||
Keywords | LYASE/LYASE INHIBITOR / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / lyase-lyase inhibitor complex / carbonate dehydratase activity / carbon-oxygen lyase activity | ||||||
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: 1.95 Å | ||||||
Authors | Smirnov, A. / Manakova, E. / Grazulis, S. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2013 Title: 4-Substituted-2,3,5,6-tetrafluorobenzenesulfonamides as inhibitors of carbonic anhydrases I, II, VII, XII, and XIII. Authors: Dudutiene, V. / Zubriene, A. / Smirnov, A. / Gylyte, J. / Timm, D. / 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 | 4hu1.cif.gz | 132.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hu1.ent.gz | 101.7 KB | Display | PDB format |
PDBx/mmJSON format | 4hu1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/4hu1 ftp://data.pdbj.org/pub/pdb/validation_reports/hu/4hu1 | HTTPS FTP |
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-Related structure data
Related structure data | 4ht0C 4ht2C 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
-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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8N1Q1, carbonic anhydrase |
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-Non-polymers , 5 types, 565 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-PEG / | #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: 2.2 Å3/Da / Density % sol: 43.7 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.1M sodium citrate pH5.5, 0.1M sodium acetate pH4.5 and 26% of PEG4000 , VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.815 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR555 flatpanel detector / Detector: FLAT PANEL / Date: Nov 15, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal Si(111), horizontally focussing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.815 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→40.178 Å / Num. all: 38614 / Num. obs: 38614 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.135 / Rsym value: 0.135 / Net I/σ(I): 9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: PDB ENTRY 2NNO Resolution: 1.95→40.178 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.916 / WRfactor Rfree: 0.232 / WRfactor Rwork: 0.166 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.851 / SU R Cruickshank DPI: 0.192 / SU Rfree: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 52.37 Å2 / Biso mean: 19.689 Å2 / Biso min: 5.74 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→40.178 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Total num. of bins used: 20
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