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Yorodumi- PDB-6yl7: Crystal structure of beta carbonic anhydrase from the pathogenic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yl7 | ||||||
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Title | Crystal structure of beta carbonic anhydrase from the pathogenic bacterium Burkholderia pseudomallei | ||||||
Components | Beta carbonic anhydrase | ||||||
Keywords | LYASE / carbonic anhydrase / beta carbonic anhydrase / Burkholderia pseudomallei | ||||||
Function / homology | Function and homology information carbon utilization / carbonic anhydrase / carbonate dehydratase activity / zinc ion binding Similarity search - Function | ||||||
Biological species | Burkholderia pseudomallei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 Å | ||||||
Authors | Angeli, A. / Ferraroni, M. | ||||||
Citation | Journal: Molecules / Year: 2020 Title: Crystal Structure of a Tetrameric Type II beta-Carbonic Anhydrase from the Pathogenic BacteriumBurkholderia pseudomallei. Authors: Angeli, A. / Ferraroni, M. / Pinteala, M. / Maier, S.S. / Simionescu, B.C. / Carta, F. / Del Prete, S. / Capasso, C. / Supuran, C.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yl7.cif.gz | 56.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yl7.ent.gz | 38.6 KB | Display | PDB format |
PDBx/mmJSON format | 6yl7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yl7_validation.pdf.gz | 634.9 KB | Display | wwPDB validaton report |
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Full document | 6yl7_full_validation.pdf.gz | 639.6 KB | Display | |
Data in XML | 6yl7_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 6yl7_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/6yl7 ftp://data.pdbj.org/pub/pdb/validation_reports/yl/6yl7 | HTTPS FTP |
-Related structure data
Related structure data | 6yjnC 4rxyS 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
#1: Protein | Mass: 28269.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (bacteria) Gene: can_1, can_2, BOC42_16450, CXQ84_19645, DF122_01465, ERS013345_01543, SAMEA1968934_03740 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A069AXA0, carbonic anhydrase |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 22% PEG 4000, 10% isopropanol, 100 mM HEPES pH 7.5 and 3% v/v 1,5-Diaminopentene di-HCl. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0399 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0399 Å / Relative weight: 1 |
Reflection | Resolution: 3.17→45.41 Å / Num. obs: 4883 / % possible obs: 99.9 % / Redundancy: 24.7 % / CC1/2: 1 / Rmerge(I) obs: 0.341 / Rpim(I) all: 0.093 / Rrim(I) all: 0.354 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 3.17→3.38 Å / Rmerge(I) obs: 2.96 / Num. unique obs: 849 / CC1/2: 1 / Rpim(I) all: 0.84 / Rrim(I) all: 3.08 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4rxy Resolution: 3.17→45.41 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.927 / SU B: 33.699 / SU ML: 0.536 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.557 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 199.45 Å2 / Biso mean: 90.296 Å2 / Biso min: 45.04 Å2
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Refinement step | Cycle: final / Resolution: 3.17→45.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.17→3.248 Å / Rfactor Rfree error: 0
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