6YEV | pdb_00006yev

Crystal structure of MsrA C206 and Trx C35S complex from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb6YEV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-03-25 Released: 2021-04-07 
• Deposition Author(s): Napolitano, S., Zyla, D., Glockshuber, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free: 
  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Models: experimental

Literature

Structure of a complex between the single-cysteine mutant MsrA C206 and Trx C35S from Escherichia coli

Napolitano, S., Zyla, D., Glockshuber, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 128.46 kDa 
• Atom Count: 8,822 
• Modeled Residue Count: 1,142 
• Deposited Residue Count: 1,175 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin 1	A [auth E], B [auth F], G	109	Escherichia coli K-12	Mutation(s): 1  Gene Names: trxA, fipA, tsnC, b3781, JW5856
UniProt
Find proteins for P0AA25 (Escherichia coli (strain K12)) Explore P0AA25  Go to UniProtKB:  P0AA25

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide methionine sulfoxide reductase MsrA	C [auth A], D [auth B], E [auth C], F [auth D]	212	Escherichia coli K-12	Mutation(s): 3  Gene Names: msrA, pms, b4219, JW4178 EC: 1.8.4.11
UniProt
Find proteins for P0A744 (Escherichia coli (strain K12)) Explore P0A744  Go to UniProtKB:  P0A744

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	H [auth A], I [auth B], J [auth C], K [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.91	α = 90
b = 139.91	β = 90
c = 218.05	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-07 
Deposition Author(s): Napolitano, S., Zyla, D., Glockshuber, R.

Revision History  

• Version 1.0: 2021-04-07
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary