5DM5 | pdb_00005dm5

Crystal structure of the hexameric thioesterase y2039 from Yersinia pestis

• PDB DOI: https://doi.org/10.2210/pdb5DM5/pdb

• Classification: HYDROLASE
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-09-08 Released: 2015-11-11 
• Deposition Author(s): Swarbrick, C.M.D., Forwood, J.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the hexameric thioesterase y2039 from Yersinia pestis

Swarbrick, C.M.D., Forwood, J.K.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 97.52 kDa 
• Atom Count: 5,475 
• Modeled Residue Count: 725 
• Deposited Residue Count: 912 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative acyl-CoA thioester hydrolase	A, B, C, D, E, F	152	Yersinia pestis	Mutation(s): 0  Gene Names: y2039, YPO2195 EC: 3.1.2
UniProt
Find proteins for A0A5P8YGN6 (Yersinia pestis) Explore A0A5P8YGN6  Go to UniProtKB:  A0A5P8YGN6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	H [auth B], I [auth C], J [auth D]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL	G [auth A], K [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.87	α = 90
b = 77.87	β = 90
c = 285.26	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-11 
Deposition Author(s): Swarbrick, C.M.D., Forwood, J.K.

Revision History  

• Version 1.0: 2015-11-11
  Type: Initial release
  
• Version 1.1: 2017-08-23
  Changes: Data collection, Derived calculations
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description