4XJK Metal Binding Protein date Jan 08, 2015
title Crystal Structure Of Mn(II) Ca(II) Na(I) Bound Calprotectin
authors C.L.Drennan, S.E.J.Bowman
compound source
Molecule: Protein S100-A8
Chain: A, C, E, G, I
Synonym: Calgranulin-A,Calprotectin L1l Subunit,Cystic Fibr Antigen,Cfag,Leukocyte L1 Complex Light Chain,Migration Inh Factor-Related Protein 8,P8,S100 Calcium-Binding Protein A8 Stone Protein Band A;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: S100a8, Caga, Cfag, Mrp8
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Protein S100-A9
Chain: B, D, F, H, J
Synonym: Calgranulin-B,Calprotectin L1h Subunit,Leukocyte L Heavy Chain,Migration Inhibitory Factor-Related Protein 14, Calcium-Binding Protein A9;
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: S100a9, Cagb, Cfag, Mrp14
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
symmetry Space Group: P 1 2 1
R_factor 0.185 R_Free 0.220
crystal
cell
length a length b length c angle alpha angle beta angle gamma
55.279 49.239 218.067 90.00 94.07 90.00
method X-Ray Diffractionresolution 1.76 Å
ligand CA, MN, NA enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E, C, I, G
  • sequestering of zinc ion

  • F, J, B, H, D
  • antioxidant activity
  • sequestering of zinc ion

  • Primary referenceManganese Binding Properties of Human Calprotectin under Conditions of High and Low Calcium: X-ray Crystallographic and Advanced Electron Paramagnetic Resonance Spectroscopic Analysis., Gagnon DM, Brophy MB, Bowman SE, Stich TA, Drennan CL, Britt RD, Nolan EM, J Am Chem Soc. 2015 Mar 4;137(8):3004-16. doi: 10.1021/ja512204s. Epub 2015 Feb, 18. PMID:25597447
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (192 Kb) [Save to disk]
  • Biological Unit Coordinates (4xjk.pdb1.gz) 74 Kb
  • Biological Unit Coordinates (4xjk.pdb2.gz) 76 Kb
  • Biological Unit Coordinates (4xjk.pdb3.gz) 78 Kb
  • LPC: Ligand-Protein Contacts for 4XJK
  • CSU: Contacts of Structural Units for 4XJK
  • Structure Factors (1610 Kb)
  • Retrieve 4XJK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4XJK from S2C, [Save to disk]
  • Re-refined 4xjk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4XJK 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 4XJK
  • 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 4XJK, from MSDmotif at EBI
  • Fold representative 4xjk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4xjk_H] [4xjk_A] [4xjk_E] [4xjk_G] [4xjk_D] [4xjk_J] [4xjk_B] [4xjk_C] [4xjk_F] [4xjk_I] [4xjk]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4XJK: [S_100 ] by SMART
  • Other resources with information on 4XJK
  • Community annotation for 4XJK at PDBWiki (http://pdbwiki.org)

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