1W6S

The high resolution structure of methanol dehydrogenase from methylobacterium extorquens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.177 
  • R-Value Observed: 0.158 

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This is version 1.4 of the entry. See complete history


Literature

The Atomic Resolution Structure of Methanol Dehydrogenase from Methylobacterium Extorquens

Williams, P.A.Coates, L.Mohammed, F.Gill, R.Erskine, P.T.Wood, S.P.Anthony, C.Cooper, J.B.

(2005) Acta Crystallogr D Biol Crystallogr 61: 75

  • DOI: https://doi.org/10.1107/S0907444904026964
  • Primary Citation of Related Structures:  
    1W6S

  • PubMed Abstract: 

    The crystal structure of methanol dehydrogenase (MDH) from Methylobacterium extorquens has been refined without stereochemical restraints at a resolution of 1.2 A. The high-resolution data have defined the conformation of the tricyclic pyrroloquinoline quinone (PQQ) cofactor ring as entirely planar. The detailed definition of the active-site geometry has shown many features that are similar to the quinohaemo-protein alcohol dehydrogenases from Comamonas testosteroni and Pseudomonas putida, both of which possess MDH-like and cytochrome c-like domains. Conserved features between the two types of PQQ-containing enzyme suggest a common pathway for electron transfer between MDH and its physiological electron acceptor cytochrome cL. A pathway for proton transfer from the active site to the bulk solvent is also suggested.


  • Organizational Affiliation

    School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, England.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
METHANOL DEHYDROGENASE SUBUNIT 1
A, C
599Methylorubrum extorquensMutation(s): 0 
EC: 1.1.99.8 (PDB Primary Data), 1.1.2.7 (UniProt)
UniProt
Find proteins for P16027 (Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1))
Explore P16027 
Go to UniProtKB:  P16027
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16027
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
METHANOL DEHYDROGENASE SUBUNIT 2
B, D
74Methylorubrum extorquensMutation(s): 0 
EC: 1.1.99.8 (PDB Primary Data), 1.1.2.7 (UniProt)
UniProt
Find proteins for P14775 (Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1))
Explore P14775 
Go to UniProtKB:  P14775
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14775
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PQQ
Query on PQQ

Download Ideal Coordinates CCD File 
E [auth A],
I [auth C]
PYRROLOQUINOLINE QUINONE
C14 H6 N2 O8
MMXZSJMASHPLLR-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
J [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
H [auth A],
K [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.177 
  • R-Value Observed: 0.158 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.9α = 86.09
b = 73.62β = 104.11
c = 88.08γ = 109.68
Software Package:
Software NamePurpose
SHELXL-97refinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-21
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-22
    Changes: Data collection, Other, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary