6AK1 | pdb_00006ak1

Crystal structure of DmoA from Hyphomicrobium sulfonivorans

• PDB DOI: https://doi.org/10.2210/pdb6AK1/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Hyphomicrobium sulfonivorans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-08-28 Released: 2018-12-12 
• Deposition Author(s): Cao, H.Y., Wang, P., Peng, M., Li, C.Y.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.202 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the dimethylsulfide monooxygenase DmoA from Hyphomicrobium sulfonivorans.

Cao, H.Y., Wang, P., Peng, M., Shao, X., Chen, X.L., Li, C.Y.

(2018) Acta Crystallogr F Struct Biol Commun 74: 781-786

• PubMed: 30511672 
• DOI: https://doi.org/10.1107/S2053230X18015844
• Primary Citation Related Structures: 
  6AK1


• PubMed Abstract: 
  

  DmoA is a monooxygenase which uses dioxygen (O ₂ ) and reduced flavin mononucleotide (FMNH ₂ ) to catalyze the oxidation of dimethylsulfide (DMS). Although it has been characterized, the structure of DmoA remains unknown. Here, the crystal structure of DmoA was determined to a resolution of 2.28 Å and was compared with those of its homologues LadA and BdsA. The results showed that their overall structures are similar: they all share a conserved TIM-barrel fold which is composed of eight α-helices and eight β-strands. In addition, they all have five additional insertions. Detailed comparison showed that the structures have notable differences despite their high sequence similarity. The substrate-binding pocket of DmoA is smaller compared with those of LadA and BdsA.

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Organizational Affiliation: 
• Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 108.5 kDa 
• Atom Count: 7,797 
• Modeled Residue Count: 932 
• Deposited Residue Count: 976 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dimethyl-sulfide monooxygenase	A, B	488	Hyphomicrobium sulfonivorans	Mutation(s): 0  Gene Names: dmoA EC: 1.14.13.131
UniProt
Find proteins for E9JFX9 (Hyphomicrobium sulfonivorans) Explore E9JFX9  Go to UniProtKB:  E9JFX9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.202 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M36AK1

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.19	α = 90
b = 163.954	β = 90
c = 116.674	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-12-12 
Deposition Author(s): Cao, H.Y., Wang, P., Peng, M., Li, C.Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31630012

Revision History  

• Version 1.0: 2018-12-12
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description