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Yorodumi- PDB-5ufc: Crystal Structure of Variable Lymphocyte Receptor (VLR) Tn4-22 wi... -
+Open data
-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 | |||||||||
Components | Tn4-22 | |||||||||
Keywords | 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 Function and homology information | |||||||||
Biological species | Petromyzon marinus (sea lamprey) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.888 Å | |||||||||
Authors | Collins, B.C. / Gunn, R.J. / McKitrick, T.R. / Cummings, R.D. / Cooper, M.D. / Herrin, B.R. / Wilson, I.A. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ufc.cif.gz | 158.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ufc.ent.gz | 122.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ufc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/5ufc ftp://data.pdbj.org/pub/pdb/validation_reports/uf/5ufc | HTTPS FTP |
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-Related structure data
Related structure data | 5ueiC 5uf1C 5uf4C 5ufbSC 5ufdC 5uffC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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.) Petromyzon marinus (sea lamprey) / Production host: Homo sapiens (human) #2: Polysaccharide | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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