1U6J

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.175 

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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 D Biol Crystallogr 61: 198-202

  • DOI: 10.1107/S0907444904030732
  • Primary Citation of Related Structures:  
    1U6I, 1U6K, 1U6J

  • 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, indicating a doubled c unit-cell parameter ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
F420-dependent methylenetetrahydromethanopterin dehydrogenase
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L
283Methanopyrus kandleriMutation(s): 0 
Gene Names: mtd
EC: 1.5.99.9 (PDB Primary Data), 1.5.98.1 (UniProt)
UniProt
Find proteins for P94951 (Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938))
Explore P94951 
Go to UniProtKB:  P94951
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.9α = 90
b = 118.9β = 90.01
c = 219.2γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MAR345data collection
XDSdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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