4PO3

Crystal structure of a C4-C4 SN3 tributyrin phosphonate inhibited by ESTERASE B from LACTOBACILLUS RHAMNOSIS

• PDB DOI: https://doi.org/10.2210/pdb4PO3/pdb

• Classification: HYDROLASE
• Organism(s): Lacticaseibacillus rhamnosus HN001
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-02-24 Released: 2014-06-11 
• Deposition Author(s): Bennett, M.D., Anderson, B.F., Norris, G.E., Colbert, D.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 0.208 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 

Literature

Crystal structure of a C4-C4 SN3 tributyrin phodphonate inhibited ESTERASE B from LACTOBACILLUS RHAMNOSIS

Bennett, M.D., Colbert, D.A., Anderson, B.F., Norris, G.E.

To be published.

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: 36.1 kDa 
• Atom Count: 2,676 
• Modelled Residue Count: 309 
• Deposited Residue Count: 317 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Esterase B	A [auth X]	317	Lacticaseibacillus rhamnosus HN001	Mutation(s): 1  Gene Names: LRH_10360
UniProt
Find proteins for B2CZF4 (Lacticaseibacillus rhamnosus HN001) Explore B2CZF4  Go to UniProtKB:  B2CZF4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HY4	B [auth X]	(2R)-2,3-dibutoxypropyl hydrogen (S)-propylphosphonate C14 H31 O5 P WAMWNDWVNQLPHK-CQSZACIVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 0.208 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.853	α = 90
b = 109.853	β = 90
c = 59.335	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-11 
Deposition Author(s): Bennett, M.D., Anderson, B.F., Norris, G.E., Colbert, D.A.

Revision History  

• Version 1.0: 2014-06-11
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description