6YD0

XFEL structure of the Soluble methane monooxygenase hydroxylase and regulatory subunit complex, from Methylosinus trichosporium OB3b, diferric state

• PDB DOI: https://doi.org/10.2210/pdb6YD0/pdb

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


• Deposited: 2020-03-19 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.190 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 

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

• DOI: https://doi.org/10.1021/jacs.0c05613

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 8-mer - A4B2C2 

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

Macromolecule Content

• Total Structure Weight: 139.87 kDa 
• Atom Count: 10,242 
• Modelled Residue Count: 1,209 
• Deposited Residue Count: 1,228 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methane monooxygenase	A [auth B]	395	Methylosinus trichosporium OB3b	Mutation(s): 0
UniProt
Find proteins for A0A2D2D5X7 (Methylosinus trichosporium OB3b) Explore A0A2D2D5X7  Go to UniProtKB:  A0A2D2D5X7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methane monooxygenase component A alpha chain	B [auth D]	526	Methylosinus trichosporium OB3b	Mutation(s): 0  EC: 1.14.13.25
UniProt
Find proteins for P27353 (Methylosinus trichosporium) Explore P27353  Go to UniProtKB:  P27353

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Methane monooxygenase	C [auth F]	169	Methylosinus trichosporium OB3b	Mutation(s): 0
UniProt
Find proteins for A0A2D2D0T0 (Methylosinus trichosporium OB3b) Explore A0A2D2D0T0  Go to UniProtKB:  A0A2D2D0T0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Methane monooxygenase regulatory protein B	D [auth G]	138	Methylosinus trichosporium OB3b	Mutation(s): 0  Gene Names: mmoB
UniProt
Find proteins for P27356 (Methylosinus trichosporium) Explore P27356  Go to UniProtKB:  P27356

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)	F [auth D], G [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.190 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.891	α = 90
b = 106.891	β = 90
c = 303.962	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
cctbx.xfel	data reduction
PHASER	phasing
cxi.merge	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-09-30 
Deposition Author(s): Srinivas, V., Hogbom, M.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2017-04018
European Research Council (ERC)	Sweden	HIGH-GEAR 724394
Knut and Alice Wallenberg Foundation	Sweden	2012.0233
Knut and Alice Wallenberg Foundation	Sweden	2017.0275
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM118030
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM08347
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM133081
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM117126
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM110501
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM126289
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	102593
Wellcome Trust	United Kingdom	210734/Z/18/Z
Royal Society	United Kingdom	RSWF-R2-182017
Department of Energy (DOE, United States)	United States	DOE BES DE-AC02-05CH11231
Department of Energy (DOE, United States)	United States	DOE BES DE-AC02-76SF00515

Revision History  

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