3DAG Oxidoreductase date May 29, 2008
title The Crystal Structure Of [Fe]-Hydrogenase Holoenzyme (Hmd) F Methanocaldococcus Jannaschii
authors O.Pilak, E.Warkentin, S.Shima, R.K.Thauer, U.Ermler
compound source
Molecule: 5,10-Methenyltetrahydromethanopterin Hydrogenase
Chain: A
Synonym: H(2)-Forming N(5),N(10)-Methylenetetrahydromethano Dehydrogenase, N(5),N(10)-Methenyltetrahydromethanopterin Hydrogenase, H(2)-Dependent Methylene-H(4)Mpt Dehydrogenase
Ec: 1.12.98.2
Engineered: Yes
Organism_scientific: Methanocaldococcus Jannaschii
Organism_common: Methanococcus Jannaschii
Organism_taxid: 2190
Strain: Dsmz2661
Gene: Hmd, Mj0784
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834 (De3)(Plyss)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet24b
symmetry Space Group: I 41 2 2
R_factor 0.179 R_Free 0.220
crystal
cell
length a length b length c angle alpha angle beta angle gamma
95.930 95.930 165.810 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.75 Å
ligand CMO, FE2, FEG enzyme Oxidoreductase E.C.1.12.98.2 BRENDA
note 3DAG (Molecule of the Month:pdb111)
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceThe crystal structure of [Fe]-hydrogenase reveals the geometry of the active site., Shima S, Pilak O, Vogt S, Schick M, Stagni MS, Meyer-Klaucke W, Warkentin E, Thauer RK, Ermler U, Science. 2008 Jul 25;321(5888):572-5. PMID:18653896
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (64 Kb) [Save to disk]
  • Biological Unit Coordinates (3dag.pdb1.gz) 116 Kb
  • LPC: Ligand-Protein Contacts for 3DAG
  • CSU: Contacts of Structural Units for 3DAG
  • Likely Quarternary Molecular Structure file(s) for 3DAG
  • Structure Factors (530 Kb)
  • Retrieve 3DAG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DAG from S2C, [Save to disk]
  • Re-refined 3dag structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DAG 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 3DAG
  • 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 3DAG, from MSDmotif at EBI
  • Fold representative 3dag from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dag] [3dag_A]
  • SWISS-PROT database: [Q58194]
  • Domain organization of [HMD_METJA] by SWISSPFAM
  • Other resources with information on 3DAG
  • Community annotation for 3DAG 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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