5SV6 | pdb_00005sv6

Crystal structure of MxaJ from Methlophaga aminisulfidivorans MPT

• PDB DOI: https://doi.org/10.2210/pdb5SV6/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Methylophaga thalassica MP
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-08-04 Released: 2017-07-12 
• Deposition Author(s): Choi, J.M., Lee, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.239 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

MxaJ structure reveals a periplasmic binding protein-like architecture with unique secondary structural elements

Choi, J.M., Cao, T.P., Kim, S.W., Lee, K.H., Lee, S.H.

(2017) Proteins 85: 1379-1386

• PubMed: 28295618 
• DOI: https://doi.org/10.1002/prot.25283
• Primary Citation Related Structures: 
  5SV6


• PubMed Abstract: 
  

  MxaJ is a component of type II methanol dehydrogenase (MDH) that mediates electron transfer during methanol oxidation in methanotrophic bacteria. However, little is known about how MxaJ structurally cooperates with MDH and Cytochrome c _L . Here, we report for the first time the crystal structure of MxaJ. MxaJ consists of eight α-helices and six β-strands, and resembles the "bi-lobate" folding architecture found in periplasmic binding proteins. Distinctive features of MxaJ include prominent loops and a β-strand around the hinge region supporting the ligand-binding cavity, which might provide a more favorable framework for interacting with proteins rather than small molecules. Proteins 2017; 85:1379-1386. © 2017 Wiley Periodicals, Inc.

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Organizational Affiliation: 
• Department of Cellular and Molecular Medicine, Chosun University School of Medicine, Gwangju, 61452, Korea.
National Research Center for Dementia, Chosun University, Gwangju, 61452, Korea.
Department of Environmental Engineering, Chosun University, Gwangju, 61452, Korea.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 32.92 kDa 
• Atom Count: 2,226 
• Modeled Residue Count: 246 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular solute-binding protein, family 3	A	291	Methylophaga thalassica MP	Mutation(s): 0  Gene Names: mxaJ
UniProt
Find proteins for A3FJ49 (Methylophaga aminisulfidivorans MP) Explore A3FJ49  Go to UniProtKB:  A3FJ49

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BR	B [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.239 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.127	α = 90
b = 63.761	β = 90
c = 99.246	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-07-12 
Deposition Author(s): Choi, J.M., Lee, S.H.

Revision History  

• Version 1.0: 2017-07-12
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Structure summary