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Yorodumi- PDB-6tku: Crystal structure of a capsule-specific depolymerase produced by ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tku | ||||||
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Title | Crystal structure of a capsule-specific depolymerase produced by Klebsiella phage | ||||||
Components | depolymerase KP32gp38 | ||||||
Keywords | HYDROLASE / Klebsiella pneumoniae capsule / phage depolymerase / tail fiber branching system | ||||||
Function / homology | Pectin lyase fold / Pectin lyase fold/virulence factor / Uncharacterized protein 38 Function and homology information | ||||||
Biological species | Klebsiella phage KP32 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Berisio, R. / Squeglia, F. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Structure / Year: 2020 Title: Structural and Functional Studies of a Klebsiella Phage Capsule Depolymerase Tailspike: Mechanistic Insights into Capsular Degradation. Authors: Squeglia, F. / Maciejewska, B. / Latka, A. / Ruggiero, A. / Briers, Y. / Drulis-Kawa, Z. / Berisio, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tku.cif.gz | 125 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tku.ent.gz | 99.5 KB | Display | PDB format |
PDBx/mmJSON format | 6tku.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tk/6tku ftp://data.pdbj.org/pub/pdb/validation_reports/tk/6tku | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: 63317.254 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella phage KP32 (virus) / Gene: 38 / Production host: Escherichia coli (E. coli) / References: UniProt: D1L2X1 |
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#2: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M Ammonium citrate tribasic pH 7.0 and 20% w/v polyethylene glycol 3,350. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.9759 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9759 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 59968 / % possible obs: 99.9 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.8→1.84 Å / Rmerge(I) obs: 0.232 / Num. unique obs: 4226 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→14.91 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.575 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.132 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
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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: 102.26 Å2 / Biso mean: 40.1911 Å2 / Biso min: 12.16 Å2
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Refinement step | Cycle: final / Resolution: 1.8→14.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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