3DYI

Snapshots of esterase D from lactobacillus rhamnosus: Insights into a rotation driven catalytic mechanism

• PDB DOI: https://doi.org/10.2210/pdb3DYI/pdb

• Classification: HYDROLASE
• Organism(s): Lacticaseibacillus rhamnosus HN001
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-07-28 Released: 2009-07-28 
• Deposition Author(s): Bennett, M.D., Delabre, M.-L., Holland, R., Norris, G.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.201 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 

Starting Model: experimental

Literature

Snapshots of esterase D from lactobacillus rhamnosus: Insights into a rotation driven catalytic mechanism

Bennett, M.D., Delabre, M.-L., Holland, R., 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: 27.36 kDa 
• Atom Count: 2,080 
• Modelled Residue Count: 240 
• Deposited Residue Count: 251 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Esterase D	A	251	Lacticaseibacillus rhamnosus HN001	Mutation(s): 0  Gene Names: EstD
UniProt
Find proteins for B2CZF3 (Lacticaseibacillus rhamnosus HN001) Explore B2CZF3  Go to UniProtKB:  B2CZF3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.201 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.442	α = 90
b = 47.442	β = 90
c = 174.18	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-28 
Deposition Author(s): Bennett, M.D., Delabre, M.-L., Holland, R., Norris, G.E.

Revision History  

• Version 1.0: 2009-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description