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- PDB-8bai: The surface-exposed lipo-protein of BtuG2 in complex with cyanoco... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8bai | ||||||
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Title | The surface-exposed lipo-protein of BtuG2 in complex with cyanocobalamin. | ||||||
![]() | Surface layer protein | ||||||
![]() | TRANSPORT PROTEIN / B12 / transport / soluble protein | ||||||
Function / homology | Protein of unknown function DUF5074 / Domain of unknown function (DUF5074) / Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / WD40/YVTN repeat-like-containing domain superfamily / CYANOCOBALAMIN / DI(HYDROXYETHYL)ETHER / Surface layer protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Whittaker, J. / Martinez Felices, J.M. / Guskov, A. / Slotboom, D.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The surface-exposed lipo-protein of BtuG2 in complex with cyanocobalamin. Authors: Whittaker, J. / Guskov, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 297 KB | Display | ![]() |
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PDB format | ![]() | 238.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 58.3 KB | Display | |
Data in CIF | ![]() | 81.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1nqgS S: Starting model for refinement |
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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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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 37183.648 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50 Gene: BT_1954 / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 811 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/CNC.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CNC.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-CNC / #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: TRIS pH 8.0, PEG4000, NaCl, MgCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→101.1 Å / Num. obs: 169723 / % possible obs: 99 % / Redundancy: 6 % / CC1/2: 0.98 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.69→8.6 Å / Num. unique obs: 169700 / CC1/2: 0.98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1NQG Resolution: 1.69→42.63 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.777 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.084 / 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: 19.03 Å2
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Refinement step | Cycle: 1 / Resolution: 1.69→42.63 Å
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Refine LS restraints |
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