4XXL Electron Transport date Jan 30, 2015
title Crystal Structure Of Class 1 Cytochrome Mtod From Sideroxyda Lithotrophicus Es-1
authors C.R.Beckwith, M.J.Edwards, T.Clarke
compound source
Molecule: Cytochrome C Class I
Chain: A
Engineered: Yes
Organism_scientific: Sideroxydans Lithotrophicus (Strain Es
Organism_taxid: 580332
Gene: Slit_2498
Expression_system: Shewanella Oneidensis Mr-1
Expression_system_taxid: 211586
symmetry Space Group: P 21 21 2
R_factor 0.190 R_Free 0.230
length a length b length c angle alpha angle beta angle gamma
92.180 40.200 29.700 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.47 Å
ligand HEC enzyme

Primary referenceCharacterization of MtoD from Sideroxydans lithotrophicus: a cytochrome c electron shuttle used in lithoautotrophic growth., Beckwith CR, Edwards MJ, Lawes M, Shi L, Butt JN, Richardson DJ, Clarke TA, Front Microbiol. 2015 Apr 28;6:332. doi: 10.3389/fmicb.2015.00332. eCollection, 2015. PMID:25972843
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (24 Kb) [Save to disk]
  • Biological Unit Coordinates (4xxl.pdb1.gz) 19 Kb
  • LPC: Ligand-Protein Contacts for 4XXL
  • CSU: Contacts of Structural Units for 4XXL
  • Structure Factors (344 Kb)
  • Retrieve 4XXL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4XXL from S2C, [Save to disk]
  • Re-refined 4xxl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4XXL 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 4XXL
  • 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 4XXL, from MSDmotif at EBI
  • Fold representative 4xxl from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4xxl] [4xxl_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4XXL
  • Community annotation for 4XXL at PDBWiki (http://pdbwiki.org)

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