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Yorodumi- PDB-4k79: Recognition of the Thomsen-Friedenreich Antigen by a Lamprey Vari... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k79 | |||||||||
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Title | Recognition of the Thomsen-Friedenreich Antigen by a Lamprey Variable Lymphocyte Receptor | |||||||||
Components | Variable lymphocyte receptor | |||||||||
Keywords | IMMUNE SYSTEM / Leucine Rich Repeat / Antigen Receptor / Thomsen-Friedenreich Antigen | |||||||||
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 N-terminal domain / 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 Similarity search - Domain/homology | |||||||||
Biological species | Petromyzon marinus (sea lamprey) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Luo, M. / Velikovsky, C.A. / Yang, X.B. / Mariuzza, R.A. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Recognition of the thomsen-friedenreich pancarcinoma carbohydrate antigen by a lamprey variable lymphocyte receptor. Authors: Luo, M. / Velikovsky, C.A. / Yang, X. / Siddiqui, M.A. / Hong, X. / Barchi, J.J. / Gildersleeve, J.C. / Pancer, Z. / Mariuzza, R.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k79.cif.gz | 180.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k79.ent.gz | 142.9 KB | Display | PDB format |
PDBx/mmJSON format | 4k79.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/4k79 ftp://data.pdbj.org/pub/pdb/validation_reports/k7/4k79 | HTTPS FTP |
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-Related structure data
Related structure data | 4k5uC 3e6jS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23928.309 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Petromyzon marinus (sea lamprey) / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: K0IE77 #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: 2.03 Å3/Da / Density % sol: 39.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% (w/v) polyethylene glycol (PEG) 3350, 4% (v/v) glycerol, and 0.1M Tris-HCl (pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 8, 2012 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→33.66 Å / Num. all: 39152 / Num. obs: 38816 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.2→2.28 Å / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3E6J Resolution: 2.2→33.66 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.899 / SU B: 7.674 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.406 / ESU R Free: 0.247 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.598 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→33.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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