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- PDB-8ol4: Structure of the C-terminal domains of the Bdellovibrio bacteriov... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ol4 | ||||||
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Title | Structure of the C-terminal domains of the Bdellovibrio bacteriovorus Bd2439 fibre in complex with GlcNAc | ||||||
![]() | Cell wall surface anchor family protein | ||||||
![]() | CELL ADHESION / Fibre / adhesin / TNF / TNF-like | ||||||
Function / homology | IODIDE ION / DI(HYDROXYETHYL)ETHER / Cell wall surface anchor family protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Caulton, S.G. / Lovering, A.L. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 325.6 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 35.3 KB | Display | |
Data in CIF | ![]() | 51.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ojnC ![]() 8ok3C ![]() 8oksC ![]() 8okwC ![]() 8omlC ![]() 8on4C ![]() 8onbC ![]() 8oncC ![]() 8ondC ![]() 8onfC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 6 molecules ABC![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 30335.496 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Bd2439 / Production host: ![]() ![]() #5: Sugar | |
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-Non-polymers , 6 types, 591 molecules ![](data/chem/img/IOD.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/B3P.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/B3P.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-PG4 / | #4: Chemical | ChemComp-PEG / #6: Chemical | ChemComp-SO4 / | #7: Chemical | ChemComp-B3P / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.33 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium iodide, 0.1 M Bis-Tris propane pH 8.5, 20 % w/v PEG 3350, 100 mM GlcNAc-MurNAc |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 24, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→80.17 Å / Num. obs: 49745 / % possible obs: 80.2 % / Redundancy: 11.8 % / CC1/2: 0.998 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.84→1.98 Å / Num. unique obs: 2487 / CC1/2: 0.664 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 1.84→45.13 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: 10.9184 Å / Origin y: 21.4548 Å / Origin z: 12.7431 Å
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Refinement TLS group | Selection details: all |