4EE9 | pdb_00004ee9

Crystal structure of the RBcel1 endo-1,4-glucanase

• PDB DOI: https://doi.org/10.2210/pdb4EE9/pdb

• Classification: HYDROLASE
• Organism(s): uncultured bacterium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-03-28 Released: 2013-04-03 
• Deposition Author(s): Delsaute, M., Berlemont, R., Van Elder, D., Galleni, M., Bauvois, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 
  0.176 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Literature

Three-dimensional structure of RBcel1, a metagenome-derived psychrotolerant family GH5 endoglucanase.

Delsaute, M., Berlemont, R., Dehareng, D., Van Elder, D., Galleni, M., Bauvois, C.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 828-833

• PubMed: 23908022 
• DOI: https://doi.org/10.1107/S1744309113014565
• Primary Citation of Related Structures:  
  4EE9


• PubMed Abstract: 
  

  RBcel1 is an endoglucanase belonging to glycoside hydrolase family 5 subfamily 5 (GH5_5) that was recently identified from a soil metagenome library from the Antarctic. Unlike its closest structural homologue (Cel5A from Thermoascus aurantiacus), this enzyme was reported to be able to catalyze transglycosylation reactions and has putatively been implicated in the bacterial cellulose-synthesis process. Here, the structure of RBcel1 at 1.4 Å resolution, solved by molecular replacement, is reported. The structure and putative substrate-binding site are described and compared with those of other GH5_5 subfamily members.

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Organizational Affiliation: 

Centre d'Ingénierie des Protéines, Laboratoire de Macromolécules Biologiques, Université de Liège (ULg), Bâtiment B6, Allée de la Chimie 3, 4000 Liège, Belgium.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 36.75 kDa 
• Atom Count: 3,237 
• Modelled Residue Count: 321 
• Deposited Residue Count: 321 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoglucanase	A	321	uncultured bacterium	Mutation(s): 0  EC: 3.2.1.4
UniProt
Find proteins for C1JI15 (uncultured bacterium) Explore C1JI15  Go to UniProtKB:  C1JI15

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	B [auth A], C [auth A], D [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free:  0.176 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.2	α = 90
b = 63.09	β = 90
c = 98.92	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-03 
Deposition Author(s): Delsaute, M., Berlemont, R., Van Elder, D., Galleni, M., Bauvois, C.

Revision History  

• Version 1.0: 2013-04-03
  Type: Initial release
  
• Version 1.1: 2013-08-14
  Changes: Database references
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary