3D00 Crystal structure of a tungsten formylmethanofuran dehydrogenase subunit e (fmde)-like protein (syn_00638) from syntrophus aciditrophicus at 1.90 A resolution date
authors JCSG, Joint.Center.for.Structural.Genomics.
compound source
symmetry
R_factor
R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.90
ligand CL, MSE, ZN enzyme
Gene SYNAS ; SYN ; YP
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved alpha+beta core domain and an auxiliary C-terminal treble-clef zinc finger., Axelrod HL, Das D, Abdubek P, Astakhova T, Bakolitsa C, Carlton D, Chen C, Chiu HJ, Clayton T, Deller MC, Duan L, Ellrott K, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Lam WW, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt, 10):1335-46. Epub 2010 Aug 4. PMID:20944230
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (36 Kb) [Save to disk]
  • Biological Unit Coordinates (3d00.pdb1.gz) 58 Kb
  • LPC: Ligand-Protein Contacts for 3D00
  • CSU: Contacts of Structural Units for 3D00
  • Likely Quarternary Molecular Structure file(s) for 3D00
  • Structure Factors (2543 Kb)
  • Retrieve 3D00 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3D00 from S2C, [Save to disk]
  • Re-refined 3d00 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3D00 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 3D00
  • 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
  • 3D motif for 3D00, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3d00] [3d00_A]
  • SWISS-PROT database: [Q2LQ23]
  • Domain organization of [Q2LQ23_SYNAS] by SWISSPFAM
    • Other resources with information on 3D00
  • Community annotation for 3D00 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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