4JO5

CBM3a-L domain with flanking linkers from scaffoldin cipA of cellulosome of Clostridium thermocellum

• PDB DOI: https://doi.org/10.2210/pdb4JO5/pdb

• Classification: CELLULOSE BINDING PROTEIN
• Organism(s): Acetivibrio thermocellus YS
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2013-03-16 Released: 2013-07-17 
• Deposition Author(s): Shimon, L.J.W., Frolow, F., Bayer, E.A., Yaniv, O., Lamed, R., Morag, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.215 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 

Literature

Structure of a family 3a carbohydrate-binding module from the cellulosomal scaffoldin CipA of Clostridium thermocellum with flanking linkers: implications for cellulosome structure.

Yaniv, O., Morag, E., Borovok, I., Bayer, E.A., Lamed, R., Frolow, F., Shimon, L.J.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 733-737

• PubMed: 23832198 
• DOI: https://doi.org/10.1107/S174430911301614X
• Primary Citation of Related Structures:  
  4JO5


• PubMed Abstract: 
  

  The cellulosome of the cellulolytic bacterium Clostridium thermocellum has a structural multi-modular protein called CipA (cellulosome-integrating protein A) that includes nine enzyme-binding cohesin modules and a family 3 cellulose-binding module (CBM3a). In the CipA protein, the CBM3a module is located between the second and third cohesin modules and is connected to them via proline/threonine-rich linkers. The structure of CBM3a with portions of the C- and N-terminal flanking linker regions, CBM3a-L, has been determined to a resolution of 1.98 Å. The structure is a β-sandwich with a structural Ca(2+) ion. The structure is consistent with the previously determined CipA CBM structure; however, the structured linker regions provide a deeper insight into the overall cellulosome structure and assembly.

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Organizational Affiliation: 

Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978 Tel Aviv, Israel.

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: 21.07 kDa 
• Atom Count: 1,515 
• Modelled Residue Count: 170 
• Deposited Residue Count: 190 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellulosome anchoring protein cohesin region	A	190	Acetivibrio thermocellus YS	Mutation(s): 0  Gene Names: CIPA, YSBL_2973

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
1MZ	I [auth A]	1-METHYLIMIDAZOLE C4 H7 N2 MCTWTZJPVLRJOU-UHFFFAOYSA-O
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	F [auth A], G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.215 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 
• Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.005	α = 90
b = 109.005	β = 90
c = 109.005	γ = 90

Software Package:

Software Name	Purpose
QUBE	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-17 
Deposition Author(s): Shimon, L.J.W., Frolow, F., Bayer, E.A., Yaniv, O., Lamed, R., Morag, E.

Revision History  

• Version 1.0: 2013-07-17
  Type: Initial release
  
• Version 1.1: 2014-02-05
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description