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Yorodumi- PDB-6skv: Crystal structure of bovine carbonic anhydrase II in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6skv | ||||||
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Title | Crystal structure of bovine carbonic anhydrase II in complex with a benzenesulfonamide-based ligand (SH2) | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / CARBONIC ANHYDRASE II / CA2 / SULFONAMIDE / COMPLEX | ||||||
Function / homology | Function and homology information positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / cyanamide hydratase / cyanamide hydratase activity / angiotensin-activated signaling pathway / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / one-carbon metabolic process ...positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / cyanamide hydratase / cyanamide hydratase activity / angiotensin-activated signaling pathway / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / one-carbon metabolic process / apical part of cell / zinc ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Groves, M.R. / Wang, W. / van Oosterwijk, N. | ||||||
Funding support | Netherlands, 1items
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Citation | Journal: To Be Published Title: Target diazotransfer reagents to label metalloenzymes Authors: Groves, M.R. / Wang, W. / van Oosterwijk, N. / Witte, M. / Lohse, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6skv.cif.gz | 124.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6skv.ent.gz | 95.2 KB | Display | PDB format |
PDBx/mmJSON format | 6skv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sk/6skv ftp://data.pdbj.org/pub/pdb/validation_reports/sk/6skv | HTTPS FTP |
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-Related structure data
Related structure data | 6sksC 6sktC 1v9eS 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29151.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: Blood / References: UniProt: P00921, carbonic anhydrase |
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-Non-polymers , 5 types, 220 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-E5Z / ~{ | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.77 Å3/Da / Density % sol: 55.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100mM HEPES pH7.5, 14% PEG3350, 20% Glycerol, 5mM CuCl2. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 18, 2017 / Details: double crystal monochromator |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→42.3 Å / Num. obs: 33253 / % possible obs: 99.98 % / Redundancy: 19.7 % / Biso Wilson estimate: 29.25 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08123 / Rpim(I) all: 0.01884 / Rrim(I) all: 0.08344 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 19.1 % / Rmerge(I) obs: 0.5524 / Mean I/σ(I) obs: 4.11 / Num. unique obs: 3277 / CC1/2: 0.966 / Rpim(I) all: 0.1292 / Rrim(I) all: 0.5675 / % possible all: 99.94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1V9E Resolution: 1.75→42.3 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.966 / SU B: 4.158 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.091 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.19 Å2 / Biso mean: 34.13 Å2 / Biso min: 22 Å2
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Refinement step | Cycle: final / Resolution: 1.75→42.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.793 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 19.3656 Å / Origin y: -14.1694 Å / Origin z: 3.0828 Å
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