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Yorodumi- PDB-8oq0: Crystal structure of tailspike depolymerase (APK09_gp48) from Aci... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8oq0 | ||||||
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Title | Crystal structure of tailspike depolymerase (APK09_gp48) from Acinetobacter phage APK09 | ||||||
Components | Tailspike protein | ||||||
Keywords | VIRAL PROTEIN / bacteriophage / Acinetobacter baumannii / tailspike depolymerase | ||||||
Function / homology | DI(HYDROXYETHYL)ETHER Function and homology information | ||||||
Biological species | Acinetobacter phage APK09 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | ||||||
Authors | Matyuta, I.O. / Boyko, K.M. / Nikolaeva, A.Y. / Shneider, M.M. / Timoshina, O.Y. / Popova, A.V. / Miroshnikov, K.A. / Popov, V.O. | ||||||
Funding support | Russian Federation, 1items
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Citation | Journal: Int J Mol Sci / Year: 2023 Title: Friunavirus Phage-Encoded Depolymerases Specific to Different Capsular Types of Acinetobacter baumannii . Authors: Timoshina, O.Y. / Kasimova, A.A. / Shneider, M.M. / Matyuta, I.O. / Nikolaeva, A.Y. / Evseev, P.V. / Arbatsky, N.P. / Shashkov, A.S. / Chizhov, A.O. / Shelenkov, A.A. / Mikhaylova, Y.V. / ...Authors: Timoshina, O.Y. / Kasimova, A.A. / Shneider, M.M. / Matyuta, I.O. / Nikolaeva, A.Y. / Evseev, P.V. / Arbatsky, N.P. / Shashkov, A.S. / Chizhov, A.O. / Shelenkov, A.A. / Mikhaylova, Y.V. / Slukin, P.V. / Volozhantsev, N.V. / Boyko, K.M. / Knirel, Y.A. / Miroshnikov, K.A. / Popova, A.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8oq0.cif.gz | 126.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8oq0.ent.gz | 98.8 KB | Display | PDB format |
PDBx/mmJSON format | 8oq0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/8oq0 ftp://data.pdbj.org/pub/pdb/validation_reports/oq/8oq0 | HTTPS FTP |
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-Related structure data
Related structure data | 8opzC 8oq1C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 66492.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter phage APK09 (virus) / Gene: B1_45 / Production host: Escherichia coli (E. coli) | ||||
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#2: Chemical | #3: 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: 2.4 Å3/Da / Density % sol: 48.67 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2% PEG200, 100mM HEPES pH 7.5, 20% tacsimate pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.7749 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7749 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→72.15 Å / Num. obs: 20409 / % possible obs: 99.1 % / Redundancy: 18.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.339 / Rpim(I) all: 0.081 / Rrim(I) all: 0.349 / Χ2: 0.99 / Net I/σ(I): 10.9 / Num. measured all: 377770 |
Reflection shell | Resolution: 2.59→2.7 Å / % possible obs: 94 % / Redundancy: 13.6 % / Rmerge(I) obs: 2.467 / Num. measured all: 31386 / Num. unique obs: 2302 / CC1/2: 0.303 / Rpim(I) all: 0.674 / Rrim(I) all: 2.566 / Χ2: 0.93 / Net I/σ(I) obs: 1.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→72.15 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 13.472 / SU ML: 0.282 / Cross valid method: THROUGHOUT / ESU R: 1.155 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.755 Å2
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Refinement step | Cycle: 1 / Resolution: 2.59→72.15 Å
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