1U6K

TLS refinement of the structure of Se-methionine labelled Coenzyme f420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) from Methanopyrus kandleri

• PDB DOI: https://doi.org/10.2210/pdb1U6K/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Methanopyrus kandleri
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2004-07-30 Released: 2005-02-01 
• Deposition Author(s): Warkentin, E., Hagemeier, C.H., Shima, S., Thauer, R.K., Ermler, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.195 
• R-Value Work: 0.178 

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

• PubMed: 15681872 
• DOI: https://doi.org/10.1107/S0907444904030732
• Primary Citation of Related Structures:  
  1U6I, 1U6J, 1U6K


• 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. 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.

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Organizational Affiliation: 

Max-Planck-Institut für Biophysik, Marie-Curie-Strasse 15, D-60439 Frankfurt am Main, Germany. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 96.74 kDa 
• Atom Count: 7,248 
• Modelled Residue Count: 846 
• Deposited Residue Count: 849 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
F420-dependent methylenetetrahydromethanopterin dehydrogenase	A, B, C	283	Methanopyrus kandleri	Mutation(s): 16  Gene Names: mtd EC: 1.5.99.9
UniProt
Find proteins for P94951 (Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)) Explore P94951  Go to UniProtKB:  P94951

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	D [auth A], E [auth A], F [auth A], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.195 
• R-Value Work: 0.178 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.1	α = 90
b = 151.2	β = 90
c = 110	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	phasing
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-01 
Deposition Author(s): Warkentin, E., Hagemeier, C.H., Shima, S., Thauer, R.K., Ermler, U.

Revision History  

• 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: Derived calculations, Version format compliance
• Version 1.3: 2022-12-21
  Changes: Database references, Derived calculations