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- PDB-5ufb: Crystal Structure of Variable Lymphocyte Receptor (VLR) Tn4-22 (Apo) -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ufb | ||||||
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Title | Crystal Structure of Variable Lymphocyte Receptor (VLR) Tn4-22 (Apo) | ||||||
![]() | Tn4-22 | ||||||
![]() | IMMUNE SYSTEM / variable lymphocyte receptors / VLR / leucine-rich repeat / LRR / adaptive immunity / sea lamprey / jawless fish / receptor / glycan binding / glycan receptor | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Collins, B.C. / Gunn, R.J. / McKitrick, T.R. / Cummings, R.D. / Cooper, M.D. / Herrin, B.R. / Wilson, I.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Insights into VLR Fine Specificity for Blood Group Carbohydrates. Authors: Collins, B.C. / Gunn, R.J. / McKitrick, T.R. / Cummings, R.D. / Cooper, M.D. / Herrin, B.R. / Wilson, I.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 | ![]() | 62.5 KB | Display | ![]() |
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PDB format | ![]() | 43.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 417.6 KB | Display | ![]() |
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Full document | ![]() | 417.6 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 14.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ueiC ![]() 5uf1C ![]() 5uf4C ![]() 5ufcC ![]() 5ufdC ![]() 5uffC ![]() 3e6jS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27718.572 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.75 Å3/Da / Density % sol: 67.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 21.6 mg/mL Tn4-22, 100 mM sodium acetate, pH 4.6, 200 mM lithium sulfate, 2.7 M sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.844→41.844 Å / Num. obs: 33959 / % possible obs: 100 % / Redundancy: 6.6 % / Rpim(I) all: 0.03 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.844→1.91 Å / Num. unique all: 20103 / Rpim(I) all: 0.41 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3E6J Resolution: 1.844→41.844 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.84
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.19 Å2 / Biso mean: 40.5862 Å2 / Biso min: 24.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.844→41.844 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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