4N5H | pdb_00004n5h

Crystal structure of ESTERASE B from Lactobacillus Rhamnosis (HN001)

• PDB DOI: https://doi.org/10.2210/pdb4N5H/pdb

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


• Deposited: 2013-10-09 Released: 2014-10-15 
• Deposition Author(s): Bennett, M.D., Holland, R., Loo, T.S., Smith, C.A., Norris, G.E., Delabre, M.-L., Anderson, B.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 
  0.174 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.139 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.140 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of ESTERASE B from Lactobacillus Rhamnosis (HN001)

Bennett, M.D., Anderson, B.F., Norris, G.E., Delabre, M.-L., Smith, C.A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 36.05 kDa 
• Atom Count: 2,840 
• Modeled Residue Count: 315 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPA	B [auth X], C [auth X], D [auth X]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N
CA	F [auth X]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	E [auth X]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.174 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.139 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.140 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.502	α = 90
b = 109.502	β = 90
c = 59.433	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: 2014-10-15 
Deposition Author(s): Bennett, M.D., Holland, R., Loo, T.S., Smith, C.A., Norris, G.E., Delabre, M.-L., Anderson, B.F.

Revision History  

• Version 1.0: 2014-10-15
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2024-04-03
  Changes: Refinement description