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- PDB-5uff: Crystal Structure of Variable Lymphocyte Receptor (VLR) RBC36 wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5uff | |||||||||
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Title | Crystal Structure of Variable Lymphocyte Receptor (VLR) RBC36 with Fucose(alpha-1-2)Lactose bound | |||||||||
![]() | RBC36 | |||||||||
![]() | IMMUNE SYSTEM / variable lymphocyte receptors / VLR / leucine-rich repeat / LRR / adaptive immunity / sea lamprey / jawless fish / receptor / glycan binding / glycan receptor | |||||||||
Function / homology | 2'-fucosyllactose![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Collins, B.C. / Gunn, R.J. / McKitrick, T.R. / Herrin, B.R. / Cummings, R.D. / Cooper, M.D. / 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 | ![]() | 59.7 KB | Display | ![]() |
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PDB format | ![]() | 39.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 822.4 KB | Display | ![]() |
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Full document | ![]() | 824.7 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 14.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ueiC ![]() 5uf1C ![]() 5uf4C ![]() 5ufbC ![]() 5ufcC ![]() 5ufdC ![]() 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: 23763.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Polysaccharide | alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / 2'-fucosyllactose |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.09 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 11.4 mg/mL RBC36, 6.9 mM fucose(alpha-1-2)lactose, 140 mM ammonium chloride, 22% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9784 Å / Relative weight: 1 |
Reflection | Resolution: 2.137→39.865 Å / Num. obs: 11758 / % possible obs: 97 % / Redundancy: 6.5 % / Rpim(I) all: 0.07 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.137→2.21 Å / Num. measured obs: 7003 / Num. unique all: 1106 / Rpim(I) all: 0.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3E6J Resolution: 2.137→39.856 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 39.58
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.69 Å2 / Biso mean: 37.6366 Å2 / Biso min: 21.08 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.137→39.856 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: 4
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