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- PDB-5ufd: Crystal Structure of Variable Lymphocyte Receptor (VLR) RBC36 (Apo) -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ufd | ||||||
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Title | Crystal Structure of Variable Lymphocyte Receptor (VLR) RBC36 (Apo) | ||||||
![]() | RBC36 | ||||||
![]() | 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. / 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 | ![]() | 110.1 KB | Display | ![]() |
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PDB format | ![]() | 82 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.6 KB | Display | ![]() |
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Full document | ![]() | 427.1 KB | Display | |
Data in XML | ![]() | 21.1 KB | Display | |
Data in CIF | ![]() | 31.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ueiC ![]() 5uf1C ![]() 5uf4C ![]() 5ufbC ![]() 5ufcC ![]() 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25143.574 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.43 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 17.3 mg/mL RBC36, 100 mM Tris, pH 8.5, 200 mM magnesium chloride, 20% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03316 Å / Relative weight: 1 |
Reflection | Resolution: 1.696→43.957 Å / Num. obs: 60711 / % possible obs: 99 % / Redundancy: 11.3 % / Rpim(I) all: 0.02 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 1.696→1.76 Å / Num. measured obs: 29524 / Num. unique all: 5444 / Rpim(I) all: 0.16 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3E6J Resolution: 1.696→43.957 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.48
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.72 Å2 / Biso mean: 22.5177 Å2 / Biso min: 12.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.696→43.957 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: 21
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