3BJ9 Immune System date Dec 03, 2007
title Crystal Structure Of The Surrogate Light Chain Variable Doma
authors L.M.Morstadt, A.A.Bohm, B.D.Stollar, J.D.Baleja
compound source
Molecule: Immunoglobulin Iota Chain, Immunoglobulin Lambda- Polypeptide 1;
Chain: 1
Fragment: Fusion Protein Consists Of Ig Domain Of Vpreb Pro J-Fragment Of Ig Lambda-5;
Synonym: Vpre, B Protein, Vpreb Protein, Cd179a Antigen, Immunoglobulin-Related Protein 14.1, Immunoglobulin Omega Polypeptide, Ig Lambda-5, Cd179b Antigen;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Vpreb1, Vpreb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De)Plyse
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pig203
symmetry Space Group: I 2 2 2
R_factor 0.181 R_Free 0.230
crystal
cell
length a length b length c angle alpha angle beta angle gamma
43.811 67.176 99.830 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand EDO enzyme
note 3BJ9 is a representative structure
Primary referenceEngineering and characterization of a single chain surrogate light chain variable domain., Morstadt L, Bohm A, Yuksel D, Kumar K, Stollar BD, Baleja JD, Protein Sci. 2008 Mar;17(3):458-65. PMID:18287279
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (27 Kb) [Save to disk]
  • Biological Unit Coordinates (3bj9.pdb1.gz) 22 Kb
  • LPC: Ligand-Protein Contacts for 3BJ9
  • CSU: Contacts of Structural Units for 3BJ9
  • Likely Quarternary Molecular Structure file(s) for 3BJ9
  • Structure Factors (154 Kb)
  • Retrieve 3BJ9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BJ9 from S2C, [Save to disk]
  • Re-refined 3bj9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3BJ9 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3BJ9
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3BJ9, from MSDmotif at EBI
  • Fold representative 3bj9 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3bj9] [3bj9_1]
  • SWISS-PROT database: [P12018]
  • Domain organization of [VPREB_HUMAN] by SWISSPFAM
  • Domain found in 3BJ9: [IGv ] by SMART
  • Other resources with information on 3BJ9
  • Community annotation for 3BJ9 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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