1KFG | pdb_00001kfg

The X-ray Crystal Structure of Cel9G from Clostridium cellulolyticum complexed with a Thio-Oligosaccharide Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1KFG/pdb

• Classification: HYDROLASE
• Organism(s): Ruminiclostridium cellulolyticum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-11-20 Released: 2003-07-15 
• Deposition Author(s): Mandelman, D., Belaich, A., Belaich, J.-P., Driguez, H., Haser, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.204 (Depositor) 
• R-Value Work: 
  0.167 (Depositor) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

The X-ray crystal structure of the multidomain endoglucanase Cel9G from Clostridium cellulolyticum complexed with natural and synthetic cello-olligosaccharides

Mandelman, D., Belaich, A., Belaich, J.-P., Aghajari, N., Driguez, H., Haser, R.

(2003) J Bacteriol 185: 4127-4135

• PubMed: 12837787 
• DOI: https://doi.org/10.1128/JB.185.14.4127-4135.2003
• Primary Citation Related Structures: 
  1G87, 1GA2, 1K72, 1KFG


• PubMed Abstract: 
  

  Complete cellulose degradation is the first step in the use of biomass as a source of renewable energy. To this end, the engineering of novel cellulase activity, the activity responsible for the hydrolysis of the beta-1,4-glycosidic bonds in cellulose, is a topic of great interest. The high-resolution X-ray crystal structure of a multidomain endoglucanase from Clostridium cellulolyticum has been determined at a 1.6-A resolution. The endoglucanase, Cel9G, is comprised of a family 9 catalytic domain attached to a family III(c) cellulose-binding domain. The two domains together form a flat platform onto which crystalline cellulose is suggested to bind and be fed into the active-site cleft for endolytic hydrolysis. To further dissect the structural basis of cellulose binding and hydrolysis, the structures of Cel9G in the presence of cellobiose, cellotriose, and a DP-10 thio-oligosaccharide inhibitor were resolved at resolutions of 1.7, 1.8, and 1.9 A, respectively.

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Organizational Affiliation: 
• Laboratoire de BioCristallographie, Institut de Biologie et Chimie des Protéines, UMR 5086, CNRS et Université Claude Bernard Lyon I, 69367 Lyon, Cedex 07, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 138.38 kDa 
• Atom Count: 10,341 
• Modeled Residue Count: 1,225 
• Deposited Residue Count: 1,228 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDOGLUCANASE G	A, B	614	Ruminiclostridium cellulolyticum	Mutation(s): 0  Gene Names: CELCCG EC: 3.2.1.4
UniProt
Find proteins for P37700 (Ruminiclostridium cellulolyticum (strain ATCC 35319 / DSM 5812 / JCM 6584 / H10)) Explore P37700  Go to UniProtKB:  P37700

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
4-thio-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-1-thio-beta-D-glucopyranose	C, D	4	N/A	N/A
Glycosylation Resources
GlyTouCan: G46656QM GlyCosmos: G46656QM

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	J [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL	K [auth A], L [auth A], R [auth B], S [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI	O [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CA	E [auth A], F [auth A], M [auth B], N [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	G [auth A], H [auth A], I [auth A], P [auth B], Q [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.204 (Depositor) 
• R-Value Work:  0.167 (Depositor) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.04	α = 93.86
b = 57.73	β = 100.83
c = 86.63	γ = 99.54

Software Package:

Software Name	Purpose
MAR345	data collection
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-07-15 
Deposition Author(s): Mandelman, D., Belaich, A., Belaich, J.-P., Driguez, H., Haser, R.

Revision History  

• Version 1.0: 2003-07-15
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.1: 2023-08-16
  Changes: Data collection, Database references, Refinement description, Structure summary