4N5I | pdb_00004n5i

Crystal Structure of a C8-C4 Sn3 Inhibited Esterase B from Lactobacillus Rhamnosis

• PDB DOI: https://doi.org/10.2210/pdb4N5I/pdb

• Classification: HYDROLASE
• Organism(s): Lacticaseibacillus rhamnosus Lc 705
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-10-09 Released: 2014-04-16 
• Deposition Author(s): Colbert, D.A., Bennett, M.D., Lun, D.J., Loo, T.S., Anderson, B.F., Norris, G.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of a C8-C4 Sn3 Inhibited Esterase B from Lactobacillus Rhamnosis

Colbert, D.A., D Bennett, M., J Lun, D., S Loo, T., F Anderson, B., E Norris, G.

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: 36.28 kDa 
• Atom Count: 2,827 
• Modeled Residue Count: 311 
• Deposited Residue Count: 317 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Esterase/lipase	A [auth X]	317	Lacticaseibacillus rhamnosus Lc 705	Mutation(s): 1  Gene Names: LC705_02872, LRH_10360

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2HD	B [auth X]	(2R)-2,3-dibutoxypropyl (R)-octylphosphinate C19 H41 O4 P NQMHEQXQHWVUHF-LJQANCHMSA-N
ACT	C [auth X], D [auth X]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.826	α = 90
b = 109.826	β = 90
c = 59.347	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: 2014-04-16 
Deposition Author(s): Colbert, D.A., Bennett, M.D., Lun, D.J., Loo, T.S., Anderson, B.F., Norris, G.E.

Revision History  

• Version 1.0: 2014-04-16
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Structure summary
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description