3D3N | pdb_00003d3n

Crystal structure of lipase/esterase (lp_2923) from Lactobacillus plantarum. Northeast Structural Genomics Consortium target LpR108

• PDB DOI: https://doi.org/10.2210/pdb3D3N/pdb

• Classification: HYDROLASE
• Organism(s): Lactiplantibacillus plantarum WCFS1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-05-12 Released: 2008-06-10 
• Deposition Author(s): Forouhar, F., Su, M., Seetharaman, J., Mao, L., Janjua, H., Xiao, R., Ciccosanti, C., Maglaqui, M., Foote, E.L., Zhao, L., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.263 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Literature

Crystal structure of lipase/esterase (lp_2923) from Lactobacillus plantarum. Northeast Structural Genomics Consortium target LpR108

Forouhar, F., Su, M., Seetharaman, J., Mao, L., Janjua, H., Xiao, R., Ciccosanti, C., Maglaqui, M., Foote, E.L., Zhao, L., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 64.11 kDa 
• Atom Count: 4,025 
• Modeled Residue Count: 499 
• Deposited Residue Count: 568 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative lipase/esterase	A, B	284	Lactiplantibacillus plantarum WCFS1	Mutation(s): 0  Gene Names: lp_2923, Aes
UniProt
Find proteins for F9US10 (Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)) Explore F9US10  Go to UniProtKB:  F9US10

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	C [auth A], E [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
CA	D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.263 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.074	α = 90
b = 93.022	β = 90
c = 95.765	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-10 
Deposition Author(s): Forouhar, F., Su, M., Seetharaman, J., Mao, L., Janjua, H., Xiao, R., Ciccosanti, C., Maglaqui, M., Foote, E.L., Zhao, L., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2008-06-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary