4TX1

The crystal structure of carbohydrate acetylesterase family member from Sinorhizobium meliloti

PDB DOI: https://doi.org/10.2210/pdb4TX1/pdb

Classification: HYDROLASE
Organism(s): Sinorhizobium meliloti 1021
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-07-02 Released: 2014-12-24
Deposition Author(s): Kim, K., Kim, S.S., Pandian, R., Ngo, T.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.188
R-Value Work: 0.155
R-Value Observed: 0.156

wwPDB Validation 3D Report Full Report

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

Literature

Structural and biochemical characterization of a carbohydrate acetylesterase from Sinorhizobium meliloti 1021.

Kim, K., Ryu, B.H., Kim, S.S., An, D.R., Ngo, T.D., Pandian, R., Kim, K.K., Kim, T.D.

(2015) FEBS Lett 589: 117-122

PubMed: 25436419 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2014.11.033
Primary Citation of Related Structures:
4TX1

PubMed Abstract:
In many microorganisms, carbohydrate acetylesterases remove the acetyl groups from various types of carbohydrates. Sm23 from Sinorhizobium meliloti is a putative member of carbohydrate esterase family 3 (CE3) in the CAZy classification system. Here, we determined the crystal structure of Sm23 at 1.75 Å resolution and investigated functional properties using biochemical methods. Furthermore, immobilized Sm23 exhibited improved stability compared with soluble Sm23, which can be used for the design of plant cell wall degrading-systems.

Organizational Affiliation

Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea.

Macromolecule Content

Total Structure Weight: 73.05 kDa
Atom Count: 5,522
Modelled Residue Count: 639
Deposited Residue Count: 675
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Esterase	A, B, C	225	Sinorhizobium meliloti 1021	Mutation(s): 0 Gene Names: R01448, SMc01033 EC: 3.1.1.2
UniProt
Find proteins for Q7APD5 (Rhizobium meliloti (strain 1021)) Explore Q7APD5 Go to UniProtKB: Q7APD5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7APD5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.188
R-Value Work: 0.155
R-Value Observed: 0.156
Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.238	α = 90
b = 126.238	β = 90
c = 191.101	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
PHASER	phasing
HKL	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-12-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-12-24
Type: Initial release
Version 1.1: 2014-12-31
Changes: Database references
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy