5MIX Immune System date Nov 29, 2016
title Extracellular Domain Of Human Cd83 - Trigonal Crystal Form
authors S.Klingl, C.Egerer-Sieber, B.Schmid, 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 Remains After The Gst-Tag Was Cleaved O First Three And Last Four Residues As Well As The Central R 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(De3)
Expression_system_taxid: 469008
Expression_system_variant: Gold Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-2t
symmetry Space Group: P 3 2 1
R_factor 0.188 R_Free 0.216
crystal
cell
length a length b length c angle alpha angle beta angle gamma
62.942 62.942 40.064 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.70 Å
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] (35 Kb) [Save to disk]
  • Biological Unit Coordinates (5mix.pdb1.gz) 29 Kb
  • CSU: Contacts of Structural Units for 5MIX
  • Structure Factors (68 Kb)
  • Retrieve 5MIX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5MIX from S2C, [Save to disk]
  • Re-refined 5mix structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5MIX 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 5MIX
  • 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 5mix from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5mix_A] [5mix]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5MIX
  • Community annotation for 5MIX at PDBWiki (http://pdbwiki.org)

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