1OCB

Structure of the wild-type cellobiohydrolase Cel6A from Humicolas insolens in complex with a fluorescent substrate

• PDB DOI:  https://doi.org/10.2210/pdb1OCB/pdb

• Classification: HYDROLASE
• Organism(s): Humicola insolens
• Expression System: Aspergillus oryzae
• Mutation(s): No 


• Deposited: 2003-02-07 Released: 2003-07-10 
• Deposition Author(s): Varrot, A., Frandsen, T.P., Von Ossowski, I., Boyer, V., Driguez, H., Schulein, M., Davies, G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.168 
• R-Value Work: 0.133 
• R-Value Observed: 0.135 

Literature

Structural Basis for Ligand Binding and Processivity in Cellobiohydrolase Cel6A from Humicola Insolens

Varrot, A., Frandsen, T.P., Von Ossowski, I., Boyer, V., Driguez, H., Schulein, M., Davies, G.J.

(2003) Structure 11: 855

• PubMed: 12842048 
• DOI: https://doi.org/10.1016/s0969-2126(03)00124-2
• Primary Citation of Related Structures:  
  1OC5, 1OC6, 1OC7, 1OCB, 1OCJ


• PubMed Abstract: 
  

The enzymatic digestion of cellulose entails intimate involvement of cellobiohydrolases, whose characteristic active-center tunnel contributes to a processive degradation of the polysaccharide. The cellobiohydrolase Cel6A displays an active site within a tunnel formed by two extended loops, which are known to open and close in response to ligand binding. Here we present five structures of wild-type and mutant forms of Cel6A from Humicola insolens in complex with nonhydrolyzable thio-oligosaccharides, at resolutions from 1.7-1.1 A, dissecting the structural accommodation of a processing substrate chain through the active center during hydrolysis. Movement of ligand is facilitated by extensive solvent-mediated interactions and through flexibility in the hydrophobic surfaces provided by a sheath of tryptophan residues.

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Organizational Affiliation: 

Department of Chemistry, University of York, Heslington, Y010 5YW, York, United Kingdom.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 83.55 kDa 
• Atom Count: 6,607 
• Modelled Residue Count: 722 
• Deposited Residue Count: 724 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CELLOBIOHYDROLASE II	A, B	362	Humicola insolens	Mutation(s): 0  Gene Names: cel6A, avi2 EC: 3.2.1.91
UniProt
Find proteins for Q9C1S9 (Humicola insolens) Explore Q9C1S9  Go to UniProtKB:  Q9C1S9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
4-amino-4-deoxy-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-methyl 4-thio-beta-D-glucopyranoside	C, E	4	N/A	N/A
Glycosylation Resources
GlyTouCan:  G84956EQ GlyCosmos:  G84956EQ

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-methyl 4-thio-beta-D-glucopyranoside	D, F	3	N/A	N/A
Glycosylation Resources
GlyTouCan:  G22306SE GlyCosmos:  G22306SE

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLG	K [auth B]	FLUORESCEINYLTHIOUREIDO C23 H18 N2 O5 S VHJFQSRUDVDTEO-UHFFFAOYSA-N
NAG	G [auth A], I [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	H [auth A], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.168 
• R-Value Work: 0.133 
• R-Value Observed: 0.135 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.763	α = 90
b = 155.681	β = 118.42
c = 51.218	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-07-10 
Deposition Author(s): Varrot, A., Frandsen, T.P., Von Ossowski, I., Boyer, V., Driguez, H., Schulein, M., Davies, G.J.

Revision History  

• Version 1.0: 2003-07-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 2.0: 2020-06-24
  Changes: Atomic model, Data collection, Derived calculations, Other
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary