1U6J

The Structure of native coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase at 2.4A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The structure of F420-dependent methylenetetrahydromethanopterin dehydrogenase: a crystallographic 'superstructure' of the selenomethionine-labelled protein crystal structure.

Warkentin, E.Hagemeier, C.H.Shima, S.Thauer, R.K.Ermler, U.

(2005) Acta Crystallogr.,Sect.D 61: 198-202

  • DOI: 10.1107/S0907444904030732
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The diffraction pattern of native protein crystals of F(420)-dependent methylenetetrahydromethanopterin dehydrogenase from Methanopyrus kandleri shows weak additional reflections compared with the selenomethionine-labelled protein crystals, indicatin ...

    The diffraction pattern of native protein crystals of F(420)-dependent methylenetetrahydromethanopterin dehydrogenase from Methanopyrus kandleri shows weak additional reflections compared with the selenomethionine-labelled protein crystals, indicating a doubled c unit-cell parameter. These reflections indicate small reorientations of the hexameric structural units, breaking the translational symmetry. TLS refinement of the selenomethionine-labelled protein structure at 1.55 A resolution revealed an anisotropic rigid-body libration of the hexameric units. The anisotropy is consistent with the static reorientation in the native protein crystals. These results are discussed as related to the crystal packing. The relation between the two structures suggests an analogy to structural changes during certain kinds of phase transitions that have been well studied in inorganic structural chemistry.


    Related Citations: 
    • Coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase (Mtd) from Methanopyrus kandleri: a methanogenic enzyme with an unusual quarternary structure.
      Hagemeier, C.H.,Shima, S.,Thauer, R.K.,Bourenkov, G.,Bartunik, H.D.,Ermler, U.
      (2003) J.Mol.Biol. 332: 1047


    Organizational Affiliation

    Max-Planck-Institut für Biophysik, Marie-Curie-Strasse 15, D-60439 Frankfurt am Main, Germany. eberhard.warkentin@mpibp-frankfurt.mpg.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
F420-dependent methylenetetrahydromethanopterin dehydrogenase
A, B, C, D, E, F, G, H, I, J, K, L
283Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)Mutation(s): 0 
Gene Names: mtd
EC: 1.5.98.1
Find proteins for P94951 (Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938))
Go to UniProtKB:  P94951
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, G, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 150.900α = 90.00
b = 118.900β = 90.01
c = 219.200γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
CNSphasing
CNSrefinement
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-02-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description