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- PDB-5ufc: Crystal Structure of Variable Lymphocyte Receptor (VLR) Tn4-22 wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ufc | |||||||||
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Title | Crystal Structure of Variable Lymphocyte Receptor (VLR) Tn4-22 with H-trisaccharide bound | |||||||||
![]() | Tn4-22 | |||||||||
![]() | IMMUNE SYSTEM / variable lymphocyte receptors / VLR / leucine-rich repeat / LRR / adaptive immunity / sea lamprey / jawless fish / receptor / glycan binding / glycan receptor | |||||||||
Function / homology | H type 2 antigen, beta anomer![]() | |||||||||
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 | ![]() | 158.1 KB | Display | ![]() |
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PDB format | ![]() | 122.9 KB | 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 | ![]() | 28.1 KB | Display | |
Data in CIF | ![]() | 40.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ueiC ![]() 5uf1C ![]() 5uf4C ![]() 5ufbSC ![]() 5ufdC ![]() 5uffC 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27718.572 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.53 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 11 mg/mL Tn4-22, 1 mM H-trisaccharide, 85 mM sodium acetate, pH 4.6, 170 mM ammonium acetate, 15% glycerol, 25.5% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 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: 1.888→49.458 Å / Num. obs: 74657 / % possible obs: 98 % / Redundancy: 9.7 % / Rpim(I) all: 0.03 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.888→1.96 Å / Num. measured obs: 57174 / Num. unique all: 6177 / Rpim(I) all: 0.35 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 5UFB Resolution: 1.888→49.458 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.5
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.75 Å2 / Biso mean: 32.69 Å2 / Biso min: 17.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.888→49.458 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: 26
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