3RFR

Crystal Structure of particulate methane monooxygenase (pMMO) from Methylocystis sp. strain M


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure and Characterization of Particulate Methane Monooxygenase from Methylocystis species Strain M.

Smith, S.M.Rawat, S.Telser, J.Hoffman, B.M.Stemmler, T.L.Rosenzweig, A.C.

(2011) Biochemistry 50: 10231-10240

  • DOI: 10.1021/bi200801z
  • Primary Citation of Related Structures:  
    3RFR, 3RGB

  • PubMed Abstract: 
  • Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria. Previous biochemical and structural studies of pMMO have focused on preparations from Methylococcus capsulatus (Bath) and Methylosinus trichosporium OB3b ...

    Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria. Previous biochemical and structural studies of pMMO have focused on preparations from Methylococcus capsulatus (Bath) and Methylosinus trichosporium OB3b. A pMMO from a third organism, Methylocystis species strain M, has been isolated and characterized. Both membrane-bound and solubilized Methylocystis sp. strain M pMMO contain ~2 copper ions per 100 kDa protomer and exhibit copper-dependent propylene epoxidation activity. Spectroscopic data indicate that Methylocystis sp. strain M pMMO contains a mixture of Cu(I) and Cu(II), of which the latter exhibits two distinct type 2 Cu(II) electron paramagnetic resonance (EPR) signals. Extended X-ray absorption fine structure (EXAFS) data are best fit with a mixture of Cu-O/N and Cu-Cu ligand environments with a Cu-Cu interaction at 2.52-2.64 Å. The crystal structure of Methylocystis sp. strain M pMMO was determined to 2.68 Å resolution and is the best quality pMMO structure obtained to date. It provides a revised model for the pmoA and pmoC subunits and has led to an improved model of M. capsulatus (Bath) pMMO. In these new structures, the intramembrane zinc/copper binding site has a different coordination environment from that in previous models.


    Organizational Affiliation

    Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PmoBA, J [auth E], K [auth I]419Methylocystis sp. MMutation(s): 0 
Gene Names: pmoB
Membrane Entity: Yes 
UniProt
Find proteins for Q9KX36 (Methylocystis sp. M)
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Go to UniProtKB:  Q9KX36
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
peptideB [auth D], C [auth H]19N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PmoAE [auth B], F, D [auth J]252Methylocystis sp. MMutation(s): 0 
Gene Names: pmoA
Membrane Entity: Yes 
UniProt
Find proteins for O06122 (Methylocystis sp. M)
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Go to UniProtKB:  O06122
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
PmoCG [auth C], H [auth G], I [auth K]256Methylocystis sp. MMutation(s): 0 
Gene Names: pmoC
Membrane Entity: Yes 
UniProt
Find proteins for Q9KX37 (Methylocystis sp. M)
Explore Q9KX37 
Go to UniProtKB:  Q9KX37
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.718α = 90
b = 178.31β = 90
c = 183.147γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-23
    Type: Initial release
  • Version 1.1: 2011-12-07
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description