[English] 日本語
Yorodumi- PDB-5uff: Crystal Structure of Variable Lymphocyte Receptor (VLR) RBC36 wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5uff | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of Variable Lymphocyte Receptor (VLR) RBC36 with Fucose(alpha-1-2)Lactose bound | |||||||||
Components | RBC36 | |||||||||
Keywords | 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 Function and homology information | |||||||||
Biological species | Petromyzon marinus (sea lamprey) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.137 Å | |||||||||
Authors | Collins, B.C. / Gunn, R.J. / McKitrick, T.R. / Herrin, B.R. / Cummings, R.D. / Cooper, M.D. / Wilson, I.A. | |||||||||
Funding support | United States, 1items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5uff.cif.gz | 59.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5uff.ent.gz | 39.3 KB | Display | PDB format |
PDBx/mmJSON format | 5uff.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/5uff ftp://data.pdbj.org/pub/pdb/validation_reports/uf/5uff | HTTPS FTP |
---|
-Related structure data
Related structure data | 5ueiC 5uf1C 5uf4C 5ufbC 5ufcC 5ufdC 3e6jS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23763.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Petromyzon marinus (sea lamprey) / Production host: Spodoptera frugiperda (fall armyworm) |
---|---|
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.09 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9784 Å |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
|