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Yorodumi- PDB-3e6j: Crystal Structure of Variable Lymphocyte Receptor (VLR) RBC36 in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3e6j | |||||||||
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Title | Crystal Structure of Variable Lymphocyte Receptor (VLR) RBC36 in Complex with H-trisaccharide | |||||||||
Components | Variable lymphocyte receptor diversity region | |||||||||
Keywords | IMMUNE SYSTEM / Variable Lymphocyte Receptors / VLR / Leucine-rich repeat / LRR / Adaptive immunity / Sea Lamprey / Jawless fish / Receptor | |||||||||
Function / homology | Function and homology information Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily ...Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta Similarity search - Domain/homology | |||||||||
Biological species | Petromyzon marinus (sea lamprey) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | |||||||||
Authors | Han, B.W. / Herrin, B.R. / Cooper, M.D. / Wilson, I.A. | |||||||||
Citation | Journal: Science / Year: 2008 Title: Antigen recognition by variable lymphocyte receptors. Authors: Han, B.W. / Herrin, B.R. / Cooper, M.D. / 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 | 3e6j.cif.gz | 68.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e6j.ent.gz | 47.6 KB | Display | PDB format |
PDBx/mmJSON format | 3e6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3e6j_validation.pdf.gz | 794.6 KB | Display | wwPDB validaton report |
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Full document | 3e6j_full_validation.pdf.gz | 795.7 KB | Display | |
Data in XML | 3e6j_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 3e6j_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/3e6j ftp://data.pdbj.org/pub/pdb/validation_reports/e6/3e6j | HTTPS FTP |
-Related structure data
Related structure data | 2r9uS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25219.775 Da / Num. of mol.: 1 / Fragment: Ectodomain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Petromyzon marinus (sea lamprey) / Gene: VLR / Plasmid: pBAC6 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 / References: UniProt: Q2VGE8*PLUS | ||||
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#2: Polysaccharide | alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / H type 2 antigen / beta anomer | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.54 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 1.9 M (NH4)2SO4, 0.1 M Sodium Citrate (pH 5.6), 0.2 M K/Na Tartrate, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 8, 2008 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing) |
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→50 Å / Num. all: 30080 / Num. obs: 28666 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.67→1.71 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 3.7 / Num. unique all: 2120 / % possible all: 71.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2R9U Resolution: 1.67→49.63 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.604 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.524 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→49.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.67→1.713 Å / Total num. of bins used: 20
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