2Y0O

The structure of a D-lyxose isomerase from the sigmaB regulon of Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb2Y0O/pdb

• Classification: ISOMERASE
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-12-07 Released: 2011-05-25 
• Deposition Author(s): Marles-Wright, J., Lewis, R.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.23 Å
• R-Value Free: 0.178 
• R-Value Work: 0.145 
• R-Value Observed: 0.147 

Literature

The Structure of a D-Lyxose Isomerase from the Sigmab Regulon of Bacillus Subtilis

Marles-Wright, J., Lewis, R.J.

(2011) Proteins 79: 2015

• PubMed: 21520290 
• DOI: https://doi.org/10.1002/prot.23028
• Primary Citation of Related Structures:  
  2Y0O

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Organizational Affiliation: 

Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle Upon Tyne NE2 4HH.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 20.82 kDa 
• Atom Count: 1,694 
• Modelled Residue Count: 171 
• Deposited Residue Count: 175 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROBABLE D-LYXOSE KETOL-ISOMERASE	A	175	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  EC: 5.3.1.15
UniProt
Find proteins for P96578 (Bacillus subtilis (strain 168)) Explore P96578  Go to UniProtKB:  P96578

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ARS	E [auth A]	ARSENIC As RBFQJDQYXXHULB-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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: 1.23 Å
• R-Value Free: 0.178 
• R-Value Work: 0.145 
• R-Value Observed: 0.147 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.716	α = 90
b = 42.619	β = 121.3
c = 65.881	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-25 
Deposition Author(s): Marles-Wright, J., Lewis, R.J.

Revision History  

• Version 1.0: 2011-05-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance