5MJ1 Immune System date Nov 29, 2016
title Extracellular Domain Of Human Cd83 - Rhombohedral Crystal Fo
authors S.Klingl, C.Egerer-Sieber, B.Schmid, S.Weiler, Y.A.Muller
compound source
Molecule: Cd83 Antigen
Chain: A
Synonym: Hcd83,B-Cell Activation Protein,Cell Surface Prote
Engineered: Yes
Mutation: Yes
Other_details: The First Four Residues (Gspg) Are Non-Nativ Of The Linker Which Remain After The Gst-Tag Was Cleaved Of Third Residue (P) Was Modeled As Alanine Due To Missing Ele Density. The First And Last Two Residues As Well As The Cen Region Were Not Visible In The Electron Density Maps.
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Dendritic Cells
Gene: Cd83
Expression_system: Escherichia Coli 'Bl21-Gold(De3)Plyss Ag
Expression_system_taxid: 866768
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-2t
symmetry Space Group: H 3 2
R_factor 0.172 R_Free 0.216
crystal
cell
length a length b length c angle alpha angle beta angle gamma
62.803 62.803 134.860 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.80 Å
ligand PEG enzyme
Primary referenceCrystal structure of the extracellular domain of the human dendritic cell surface marker CD83., Heilingloh CS, Klingl S, Egerer-Sieber C, Schmid B, Weiler S, Muhl-Zurbes P, Hofmann J, Stump JD, Sticht H, Kummer M, Steinkasserer A, Muller YA, J Mol Biol. 2017 Mar 14. pii: S0022-2836(17)30113-4. doi:, 10.1016/j.jmb.2017.03.009. PMID:28315353
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (36 Kb) [Save to disk]
  • Biological Unit Coordinates (5mj1.pdb1.gz) 30 Kb
  • LPC: Ligand-Protein Contacts for 5MJ1
  • CSU: Contacts of Structural Units for 5MJ1
  • Structure Factors (68 Kb)
  • Retrieve 5MJ1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5MJ1 from S2C, [Save to disk]
  • Re-refined 5mj1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5MJ1 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 5MJ1
  • 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
  • Fold representative 5mj1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5mj1] [5mj1_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5MJ1
  • Community annotation for 5MJ1 at PDBWiki (http://pdbwiki.org)

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