6SYM | pdb_00006sym

Crystal structure of Escherichia coli MsrB (reduced form)

• PDB DOI: https://doi.org/10.2210/pdb6SYM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-09-30 Released: 2020-10-14 
• Deposition Author(s): Napolitano, S., Zyla, D., Glockshuber, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 
  0.250 (DCC) 
• R-Value Work: 
  0.220 (DCC) 

Starting Model: in silico

Literature

Structure of Peptide methionine sulfoxide reductase MsrB at 1.63 Angstrom resolution

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

To be published.

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: 31.31 kDa 
• Atom Count: 2,286 
• Modeled Residue Count: 269 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide methionine sulfoxide reductase MsrB	A, B	137	Escherichia coli K-12	Mutation(s): 0  Gene Names: msrB, yeaA, b1778, JW1767 EC: 1.8.4.12
UniProt
Find proteins for P0A746 (Escherichia coli (strain K12)) Explore P0A746  Go to UniProtKB:  P0A746

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAF	A, B	L-PEPTIDE LINKING	C5 H12 As N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free:  0.250 (DCC) 
• R-Value Work:  0.220 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.39	α = 90
b = 56.27	β = 90
c = 85.61	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-10-14 
Deposition Author(s): Napolitano, S., Zyla, D., Glockshuber, R.

Revision History  

• Version 1.0: 2020-10-14
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary