3ZFS Oxidoreductase date Dec 12, 2012
title Cryo-Em Structure Of The F420-Reducing Nife-Hydrogenase From Methanogenic Archaeon With Bound Substrate
authors D.J.Mills, S.Vitt, M.Strauss, S.Shima, J.Vonck
compound source
Molecule: F420-Reducing Hydrogenase, Subunit Alpha
Chain: A
Synonym: Frha, Coenzyme F420 Hydrogenase Alpha Subunit
Ec: 1.12.98.1
Other_details: Frha Contains A Nife Center
 Organism_scientific: Methanothermobacter Marburgensis
Organism_taxid: 145263
Strain: Dsm 2133

Molecule: F420-Reducing Hydrogenase, Subunit Gamma
Chain: B
Synonym: Frhg, Coenzyme F420 Hydrogenase Gamma Subunit
Ec: 1.12.98.1
Other_details: Frhg Contains Three 4fe4s Clusters
Organism_scientific: Methanothermobacter Marburgensis
Organism_taxid: 145263
Strain: Dsm 2133

Molecule: F420-Reducing Hydrogenase, Subunit Beta
Chain: C
Synonym: Frhb, Coenzyme F420 Hydrogenase Beta Subunit
Ec: 1.12.98.1
Other_details: Frhb Contains Fad And A 4fe4s Cluster
Organism_scientific: Methanothermobacter Marburgensis
Organism_taxid: 145263
Strain: Dsm 2133
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 4.00 Å
ligand F42, FAD, FCO, FE2, NI, SF4 enzyme Oxidoreductase E.C.1.12.98.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


Primary referenceDe novo modeling of the F420-reducing [NiFe]-hydrogenase from a methanogenic archaeon by cryo-electron microscopy., Mills DJ, Vitt S, Strauss M, Shima S, Vonck J, Elife. 2013;2:e00218. doi: 10.7554/eLife.00218. Epub 2013 Mar 5. PMID:23483797
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (27 Kb) [Save to disk]
  • Biological Unit Coordinates (3zfs.pdb1.gz) 23 Kb
  • LPC: Ligand-Protein Contacts for 3ZFS
  • CSU: Contacts of Structural Units for 3ZFS
  • Retrieve 3ZFS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ZFS from S2C, [Save to disk]
    • View 3ZFS 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 3ZFS
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3ZFS, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3zfs] [3zfs_C] [3zfs_B] [3zfs_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3ZFS
  • Community annotation for 3ZFS at PDBWiki (http://pdbwiki.org)

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