+Open data
-Basic information
Entry | Database: PDB / ID: 8bbu | ||||||
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Title | Crystal structure of medical leech destabilase (high salt) | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / lysozyme / muramidase / isopeptidase / glycosidase / antibacterial | ||||||
Function / homology | Function and homology information cytolysis / metabolic process / lysozyme / lysozyme activity / defense response to bacterium Similarity search - Function | ||||||
Biological species | Hirudo medicinalis (medicinal leech) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Marin, E. / Bukhdruker, S. / Manuvera, V. / Kornilov, D. / Zinovev, E. / Bobrovsky, P. / Lazarev, V. / Borshchevskiy, V. | ||||||
Funding support | Russian Federation, 1items
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Citation | Journal: Sci Rep / Year: 2023 Title: Structural insights into thrombolytic activity of destabilase from medicinal leech. Authors: Marin, E. / Kornilov, D.A. / Bukhdruker, S.S. / Aleksenko, V.A. / Manuvera, V.A. / Zinovev, E.V. / Kovalev, K.V. / Shevtsov, M.B. / Talyzina, A.A. / Bobrovsky, P.A. / Kuzmichev, P.K. / ...Authors: Marin, E. / Kornilov, D.A. / Bukhdruker, S.S. / Aleksenko, V.A. / Manuvera, V.A. / Zinovev, E.V. / Kovalev, K.V. / Shevtsov, M.B. / Talyzina, A.A. / Bobrovsky, P.A. / Kuzmichev, P.K. / Mishin, A.V. / Gushchin, I.Y. / Lazarev, V.N. / Borshchevskiy, V.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bbu.cif.gz | 157.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bbu.ent.gz | 103.4 KB | Display | PDB format |
PDBx/mmJSON format | 8bbu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bbu_validation.pdf.gz | 459 KB | Display | wwPDB validaton report |
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Full document | 8bbu_full_validation.pdf.gz | 459.8 KB | Display | |
Data in XML | 8bbu_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 8bbu_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/8bbu ftp://data.pdbj.org/pub/pdb/validation_reports/bb/8bbu | HTTPS FTP |
-Related structure data
Related structure data | 2dqaS S: Starting model for refinement |
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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: 13697.699 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hirudo medicinalis (medicinal leech) / Plasmid: pcDNA3.4 TOPO / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q25091, lysozyme #2: Chemical | #3: Chemical | ChemComp-MLI / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.11 Å3/Da / Density % sol: 41.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 2.9 M sodium malonate, 6.4 mM NNN-triacetylchitotriose |
-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: 0.97242 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 9, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97242 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.1→34.43 Å / Num. obs: 82406 / % possible obs: 90.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 9.4 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.079 / Net I/σ(I): 9.22 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DQA Resolution: 1.1→34.43 Å / SU ML: 0.0792 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 14.847 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.75 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→34.43 Å
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Refine LS restraints |
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LS refinement shell |
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