3QM1

CRYSTAL STRUCTURE OF THE LACTOBACILLUS JOHNSONII CINNAMOYL ESTERASE LJ0536 S106A MUTANT IN COMPLEX WITH ETHYLFERULATE, Form II

PDB DOI: https://doi.org/10.2210/pdb3QM1/pdb

Classification: HYDROLASE
Organism(s): Lactobacillus johnsonii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2011-02-03 Released: 2011-08-31
Deposition Author(s): Stogios, P.J., Lai, K.K., Vu, C., Xu, X., Cui, H., Molloy, S., Gonzalez, C.F., Yakunin, A., Savchenko, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.190
R-Value Work: 0.147
R-Value Observed: 0.149

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

An Inserted alpha/beta Subdomain Shapes the Catalytic Pocket of Lactobacillus johnsonii Cinnamoyl Esterase

Lai, K.K., Stogios, P.J., Vu, C., Xu, X., Cui, H., Molloy, S., Savchenko, A., Yakunin, A., Gonzalez, C.F.

(2011) PLoS One 6: e23269-e23269

PubMed: 21876742 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0023269
Primary Citation of Related Structures:
3PF8, 3PF9, 3PFB, 3PFC, 3QM1, 3S2Z

PubMed Abstract:
Microbial enzymes produced in the gastrointestinal tract are primarily responsible for the release and biochemical transformation of absorbable bioactive monophenols. In the present work we described the crystal structure of LJ0536, a serine cinnamoyl esterase produced by the probiotic bacterium Lactobacillus johnsonii N6.2.

Organizational Affiliation

Department of Microbiology and Cell Science, Genetics Institute, University of Florida, Gainesville, Florida, United States of America.

Macromolecule Content

Total Structure Weight: 31.31 kDa
Atom Count: 2,236
Modelled Residue Count: 250
Deposited Residue Count: 265
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cinnamoyl esterase	A	265	Lactobacillus johnsonii	Mutation(s): 1 Gene Names: LJ0536 EC: 3.1.1
UniProt
Find proteins for D3YEX6 (Lactobacillus johnsonii) Explore D3YEX6 Go to UniProtKB: D3YEX6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D3YEX6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZYC Query on ZYC Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	ethyl (2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enoate C₁₂ H₁₄ O₄ ATJVZXXHKSYELS-FNORWQNLSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AB [auth A] SDF format, chain BB [auth A] SDF format, chain CB [auth A] SDF format, chain DB [auth A] SDF format, chain EB [auth A] SDF format, chain FB [auth A] SDF format, chain GB [auth A] SDF format, chain HB [auth A] SDF format, chain IB [auth A] SDF format, chain JB [auth A] SDF format, chain KB [auth A] SDF format, chain SA [auth A] SDF format, chain TA [auth A] SDF format, chain UA [auth A] SDF format, chain VA [auth A] SDF format, chain WA [auth A] SDF format, chain XA [auth A] SDF format, chain YA [auth A] SDF format, chain ZA [auth A] MOL2 format, chain AB [auth A] MOL2 format, chain BB [auth A] MOL2 format, chain CB [auth A] MOL2 format, chain DB [auth A] MOL2 format, chain EB [auth A] MOL2 format, chain FB [auth A] MOL2 format, chain GB [auth A] MOL2 format, chain HB [auth A] MOL2 format, chain IB [auth A] MOL2 format, chain JB [auth A] MOL2 format, chain KB [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain TA [auth A] MOL2 format, chain UA [auth A] MOL2 format, chain VA [auth A] MOL2 format, chain WA [auth A] MOL2 format, chain XA [auth A] MOL2 format, chain YA [auth A] MOL2 format, chain ZA [auth A]	AB [auth A] BB [auth A] CB [auth A] DB [auth A] EB [auth A] AB [auth A], BB [auth A], CB [auth A], DB [auth A], EB [auth A], FB [auth A], GB [auth A], HB [auth A], IB [auth A], JB [auth A], KB [auth A], SA [auth A], TA [auth A], UA [auth A], VA [auth A], WA [auth A], XA [auth A], YA [auth A], ZA [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AB [auth A] Focus chain BB [auth A] Focus chain CB [auth A] Focus chain DB [auth A] Focus chain EB [auth A] Focus chain FB [auth A] Focus chain GB [auth A] Focus chain HB [auth A] Focus chain IB [auth A] Focus chain JB [auth A] Focus chain KB [auth A] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain VA [auth A] Focus chain WA [auth A] Focus chain XA [auth A] Focus chain YA [auth A] Focus chain ZA [auth A] Interactions & Density Focus chain AB [auth A] Focus chain BB [auth A] Focus chain CB [auth A] Focus chain DB [auth A] Focus chain EB [auth A] Focus chain FB [auth A] Focus chain GB [auth A] Focus chain HB [auth A] Focus chain IB [auth A] Focus chain JB [auth A] Focus chain KB [auth A] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain VA [auth A] Focus chain WA [auth A] Focus chain XA [auth A] Focus chain YA [auth A] Focus chain ZA [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain C [auth A] SDF format, chain CA [auth A] SDF format, chain D [auth A] SDF format, chain DA [auth A] SDF format, chain E [auth A] SDF format, chain EA [auth A] SDF format, chain F [auth A] SDF format, chain FA [auth A] SDF format, chain G [auth A] SDF format, chain GA [auth A] SDF format, chain H [auth A] SDF format, chain HA [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth A] SDF format, chain P [auth A] SDF format, chain PA [auth A] SDF format, chain Q [auth A] SDF format, chain QA [auth A] SDF format, chain R [auth A] SDF format, chain RA [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain C [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain D [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A]	AA [auth A] BA [auth A] C [auth A] CA [auth A] D [auth A] AA [auth A], BA [auth A], C [auth A], CA [auth A], D [auth A], DA [auth A], E [auth A], EA [auth A], F [auth A], FA [auth A], G [auth A], GA [auth A], H [auth A], HA [auth A], I [auth A], IA [auth A], J [auth A], JA [auth A], K [auth A], KA [auth A], L [auth A], LA [auth A], M [auth A], MA [auth A], N [auth A], NA [auth A], O [auth A], OA [auth A], P [auth A], PA [auth A], Q [auth A], QA [auth A], R [auth A], RA [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain C [auth A] Focus chain CA [auth A] Focus chain D [auth A] Focus chain DA [auth A] Focus chain E [auth A] Focus chain EA [auth A] Focus chain F [auth A] Focus chain FA [auth A] Focus chain G [auth A] Focus chain GA [auth A] Focus chain H [auth A] Focus chain HA [auth A] Focus chain I [auth A] Focus chain IA [auth A] Focus chain J [auth A] Focus chain JA [auth A] Focus chain K [auth A] Focus chain KA [auth A] Focus chain L [auth A] Focus chain LA [auth A] Focus chain M [auth A] Focus chain MA [auth A] Focus chain N [auth A] Focus chain NA [auth A] Focus chain O [auth A] Focus chain OA [auth A] Focus chain P [auth A] Focus chain PA [auth A] Focus chain Q [auth A] Focus chain QA [auth A] Focus chain R [auth A] Focus chain RA [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain C [auth A] Focus chain CA [auth A] Focus chain D [auth A] Focus chain DA [auth A] Focus chain E [auth A] Focus chain EA [auth A] Focus chain F [auth A] Focus chain FA [auth A] Focus chain G [auth A] Focus chain GA [auth A] Focus chain H [auth A] Focus chain HA [auth A] Focus chain I [auth A] Focus chain IA [auth A] Focus chain J [auth A] Focus chain JA [auth A] Focus chain K [auth A] Focus chain KA [auth A] Focus chain L [auth A] Focus chain LA [auth A] Focus chain M [auth A] Focus chain MA [auth A] Focus chain N [auth A] Focus chain NA [auth A] Focus chain O [auth A] Focus chain OA [auth A] Focus chain P [auth A] Focus chain PA [auth A] Focus chain Q [auth A] Focus chain QA [auth A] Focus chain R [auth A] Focus chain RA [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.190
R-Value Work: 0.147
R-Value Observed: 0.149
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.872	α = 90
b = 85.396	β = 90
c = 81.142	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-08-31

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-08-31
Type: Initial release
Version 1.1: 2012-10-24
Changes: Database references
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description