4XWL | pdb_00004xwl

Catalytic domain of Clostridium Cellulovorans Exgs

• PDB DOI: https://doi.org/10.2210/pdb4XWL/pdb
• Entry: 4XWL supersedes: 4KIH

• Classification: HYDROLASE
• Organism(s): Clostridium cellulovorans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-01-29 Released: 2015-10-28 
• Deposition Author(s): liaw, Y.-C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.174 (Depositor), 0.175 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.145 (DCC) 
• R-Value Observed: 
  0.143 (Depositor) 

Starting Model: experimental

Literature

Structures of exoglucanase from Clostridium cellulovorans: cellotetraose binding and cleavage

Tsai, L.-C., Amiraslanov, I., Chen, H.R., Chen, Y.W., Lee, H.L., Liang, P.H., Liaw, Y.-C.

(2015) Acta Crystallogr F Struct Biol Commun 71: 1264-1272

• PubMed: 26457517 
• DOI: https://doi.org/10.1107/S2053230X15015915
• Primary Citation Related Structures: 
  4XWL, 4XWM, 4XWN


• PubMed Abstract: 
  

  Exoglucanase/cellobiohydrolase (EC 3.2.1.176) hydrolyzes a β-1,4-glycosidic bond from the reducing end of cellulose and releases cellobiose as the major product. Three complex crystal structures of the glycosyl hydrolase 48 (GH48) cellobiohydrolase S (ExgS) from Clostridium cellulovorans with cellobiose, cellotetraose and triethylene glycol molecules were solved. The product cellobiose occupies subsites +1 and +2 in the open active-site cleft of the enzyme-cellotetraose complex structure, indicating an enzymatic hydrolysis function. Moreover, three triethylene glycol molecules and one pentaethylene glycol molecule are located at active-site subsites -2 to -6 in the structure of the ExgS-triethylene glycol complex shown here. Modelling of glucose into subsite -1 in the active site of the ExgS-cellobiose structure revealed that Glu50 acts as a proton donor and Asp222 plays a nucleophilic role.

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Organizational Affiliation: 
• Molecular Science and Engineering, National Taipei University of Technology, 1, Section 3, Chung-Hsiao E. Road, Taipei 10608, Taiwan.
Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Taipei 11529, Taiwan.
Institute of Molecular Biology, Academia Sinica, 128 Academia Road, Section 2, Taipei 11529, Taiwan.

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: 78.61 kDa 
• Atom Count: 5,756 
• Modeled Residue Count: 634 
• Deposited Residue Count: 681 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exoglucanase S	A	681	Clostridium cellulovorans	Mutation(s): 0  Gene Names: exgS EC: 3.2.1.91
UniProt
Find proteins for O65986 (Clostridium cellulovorans) Explore O65986  Go to UniProtKB:  O65986

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P33	F [auth A]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C14 H30 O8 XPJRQAIZZQMSCM-UHFFFAOYSA-N
1PE	K [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PG4	E [auth A], G [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	H [auth A], I [auth A], J [auth A], M [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	B [auth A], C [auth A], D [auth A], L [auth A], N [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	W [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	X [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.174 (Depositor), 0.175 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.145 (DCC) 
• R-Value Observed: 0.143 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.243	α = 90
b = 108.243	β = 90
c = 182.989	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-28 
Deposition Author(s): liaw, Y.-C.
• This entry supersedes: 4KIH

Revision History  

• Version 1.0: 2015-10-28
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary