6YDU

XFEL structure of the Soluble methane monooxygenase hydroxylase and regulatory subunit complex, from Methylosinus trichosporium OB3b, reoxidized diferric state, 10s O2 exposure.

  • Classification: OXIDOREDUCTASE
  • Organism(s): Methylosinus trichosporium OB3b
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2020-03-21 Released: 2020-09-30 
  • Deposition Author(s): Srinivas, V., Hogbom, M.
  • Funding Organization(s): Swedish Research Council, European Research Council (ERC), Knut and Alice Wallenberg Foundation, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Biotechnology and Biological Sciences Research Council (BBSRC), Wellcome Trust, Royal Society, Department of Energy (DOE, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.169 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

High-Resolution XFEL Structure of the Soluble Methane Monooxygenase Hydroxylase Complex with its Regulatory Component at Ambient Temperature in Two Oxidation States.

Srinivas, V., Banerjee, R., Lebrette, H., Jones, J.C., Aurelius, O., Kim, I.S., Pham, C.C., Gul, S., Sutherlin, K.D., Bhowmick, A., John, J., Bozkurt, E., Fransson, T., Aller, P., Butryn, A., Bogacz, I., Simon, P., Keable, S., Britz, A., Tono, K., Kim, K.S., Park, S.Y., Lee, S.J., Park, J., Alonso-Mori, R., Fuller, F.D., Batyuk, A., Brewster, A.S., Bergmann, U., Sauter, N.K., Orville, A.M., Yachandra, V.K., Yano, J., Lipscomb, J.D., Kern, J., Hogbom, M.

(2020) J Am Chem Soc 142: 14249-14266


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methane monooxygenaseA [auth B]395Methylosinus trichosporium OB3bMutation(s): 0 
UniProt
Find proteins for A0A2D2D5X7 (Methylosinus trichosporium OB3b)
Explore A0A2D2D5X7 
Go to UniProtKB:  A0A2D2D5X7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2D2D5X7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Methane monooxygenase component A alpha chainB [auth D]526Methylosinus trichosporium OB3bMutation(s): 0 
EC: 1.14.13.25
UniProt
Find proteins for P27353 (Methylosinus trichosporium)
Explore P27353 
Go to UniProtKB:  P27353
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27353
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Methane monooxygenaseC [auth F]169Methylosinus trichosporium OB3bMutation(s): 0 
UniProt
Find proteins for A0A2D2D0T0 (Methylosinus trichosporium OB3b)
Explore A0A2D2D0T0 
Go to UniProtKB:  A0A2D2D0T0
Entity Groups  
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UniProt GroupA0A2D2D0T0
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Methane monooxygenase regulatory protein BD [auth G]138Methylosinus trichosporium OB3bMutation(s): 0 
Gene Names: mmoB
UniProt
Find proteins for P27356 (Methylosinus trichosporium)
Explore P27356 
Go to UniProtKB:  P27356
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27356
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.169 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.922α = 90
b = 106.922β = 90
c = 304.082γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
cctbx.xfeldata reduction
PHASERphasing
cxi.mergedata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2017-04018
European Research Council (ERC)SwedenHIGH-GEAR 724394
Knut and Alice Wallenberg FoundationSweden2012.0233
Knut and Alice Wallenberg FoundationSweden2017.0275
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118030
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM08347
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM133081
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM117126
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM110501
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM126289
Biotechnology and Biological Sciences Research Council (BBSRC)United Kingdom102593
Wellcome TrustUnited Kingdom210734/Z/18/Z
Royal SocietyUnited KingdomRSWF-R2-182017
Department of Energy (DOE, United States)United StatesDOE BES DE-AC02-05CH11231
Department of Energy (DOE, United States)United StatesDOE BES DE-AC02-76SF00515

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description