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Yorodumi- PDB-8onc: Structure of the C-terminal beta helix domain of the Bdellovibrio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8onc | ||||||
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Title | Structure of the C-terminal beta helix domain of the Bdellovibrio bacteriovorus Bd3182 fibre | ||||||
Components | Cell wall surface anchor family protein | ||||||
Keywords | CELL ADHESION / Fibre / adhesin | ||||||
Function / homology | : / Intramolecular chaperone auto-processing domain / Chaperone of endosialidase / Intramolecular chaperone auto-processing (ICA) domain profile. / protein autoprocessing / sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / Cell wall surface anchor family protein Function and homology information | ||||||
Biological species | Bdellovibrio bacteriovorus HD100 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Caulton, S.G. / Lovering, A.L. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Microbiol / Year: 2024 Title: Bdellovibrio bacteriovorus uses chimeric fibre proteins to recognize and invade a broad range of bacterial hosts. Authors: Caulton, S.G. / Lambert, C. / Tyson, J. / Radford, P. / Al-Bayati, A. / Greenwood, S. / Banks, E.J. / Clark, C. / Till, R. / Pires, E. / Sockett, R.E. / Lovering, A.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8onc.cif.gz | 341.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8onc.ent.gz | 278.8 KB | Display | PDB format |
PDBx/mmJSON format | 8onc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8onc_validation.pdf.gz | 478.9 KB | Display | wwPDB validaton report |
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Full document | 8onc_full_validation.pdf.gz | 482.9 KB | Display | |
Data in XML | 8onc_validation.xml.gz | 37 KB | Display | |
Data in CIF | 8onc_validation.cif.gz | 53 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/8onc ftp://data.pdbj.org/pub/pdb/validation_reports/on/8onc | HTTPS FTP |
-Related structure data
Related structure data | 8ojnC 8ok3C 8oksC 8okwC 8ol4C 8omlC 8on4C 8onbC 8ondC 8onfC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15519.053 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bdellovibrio bacteriovorus HD100 (bacteria) Gene: Bd3182 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6MIH5 #2: Chemical | ChemComp-EDO / | #3: 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: 2.37 Å3/Da / Density % sol: 48.14 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 1.0 M sodium citrate tribasic dihydrate, 0.1 M HEPES pH 7. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 28, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2→79.41 Å / Num. obs: 59598 / % possible obs: 100 % / Redundancy: 6.1 % / CC1/2: 0.997 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2→2.05 Å / Num. unique obs: 4316 / CC1/2: 0.879 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→79.41 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.08 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→79.41 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -12.7099 Å / Origin y: -7.187 Å / Origin z: 42.754 Å
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Refinement TLS group | Selection details: all |