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)

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)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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.

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

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F9US10
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-06-10

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

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