4TX1 | pdb_00004tx1

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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.155 (Depositor) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

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 
• DOI: https://doi.org/10.1016/j.febslet.2014.11.033
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea.
Department of Applied Chemistry and Biological Engineering, College of Engineering, Ajou University, Suwon 443-741, Republic of Korea.
Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea. Electronic address: [e-mail].
Department of Applied Chemistry and Biological Engineering, College of Engineering, Ajou University, Suwon 443-741, Republic of Korea. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

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

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.155 (Depositor) 
• R-Value Observed: 0.156 (Depositor) 

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

Entry History 

Deposition Data

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

Revision History  

• 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