1GKK

Feruloyl esterase domain of XynY from clostridium thermocellum

• PDB DOI:  https://doi.org/10.2210/pdb1GKK/pdb

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


• Deposited: 2001-08-15 Released: 2001-12-13 
• Deposition Author(s): Prates, J.A.M., Tarbouriech, N., Charnock, S.J., Fontes, C.M.G.A., Ferreira, L.M.A., Davies, G.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.173 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 

Literature

The Structure of the Feruloyl Esterase Module of Xylanase 10B from Clostridium Thermocellum Provides Insights Into Substrate Recognition

Prates, J.A.M., Tarbouriech, N., Charnock, S.J., Fontes, C.M.G.A., Ferreira, L.M.A., Davies, G.J.

(2001) Structure 9: 1183

• PubMed: 11738044 
• DOI: https://doi.org/10.1016/s0969-2126(01)00684-0
• Primary Citation of Related Structures:  
  1GKK, 1GKL


• PubMed Abstract: 
  

Degradation of the plant cell wall requires the synergistic action of a consortium of predominantly modular enzymes. In Clostridiae, these biocatalysts are organized into a supramolecular assembly termed a "cellulosome." This multienzyme complex possesses, in addition to its well-described cellulolytic activity, an apparatus specific for xylan degradation. Cinnamic acid esterases hydrolyze the ferulate groups involved in the crosslinking of arabinoxylans to lignin and thus play a key role in the degradation of the plant cell wall in addition to having promising industrial and medical applications.

---

Organizational Affiliation: 

Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veteterinária, Pólo Universitário do Alto da Ajuda, 1300-477 Lisboa Codex, Portugal.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 69.75 kDa 
• Atom Count: 5,422 
• Modelled Residue Count: 566 
• Deposited Residue Count: 594 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDO-1,4-BETA-XYLANASE Y	A, B	297	Acetivibrio thermocellus	Mutation(s): 0  Gene Names: xynY EC: 3.2.1.8
UniProt
Find proteins for P51584 (Acetivibrio thermocellus) Explore P51584  Go to UniProtKB:  P51584

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
GOL	M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET
SEP	A, B	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.173 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.381	α = 90
b = 108.793	β = 90
c = 113.877	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
TRUNCATE	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-12-13 
Deposition Author(s): Prates, J.A.M., Tarbouriech, N., Charnock, S.J., Fontes, C.M.G.A., Ferreira, L.M.A., Davies, G.J.

Revision History  

• Version 1.0: 2001-12-13
  Type: Initial release
  
• Version 1.1: 2011-09-07
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance