Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 23.19 kDa 
• Atom Count: 1898 
• Modelled Residue Count: 193 
• Deposited Residue Count: 203 
• Unique protein chains: 1

3ACH

Crystal Structure of Carbohydrate-Binding Module Family 28 from Clostridium josui Cel5A in complex with cellotetraose

• PDB DOI: 10.2210/pdb3ACH/pdb

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


• Deposited: 2010-01-04 Released: 2010-03-02 
• Deposition Author(s): Tsukimoto, K., Takada, R., Araki, Y., Suzuki, K., Karita, S., Wakagi, T., Shoun, H., Watanabe, T., Fushinobu, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.198 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 

Literature

Recognition of cellooligosaccharides by a family 28 carbohydrate-binding module.

Tsukimoto, K., Takada, R., Araki, Y., Suzuki, K., Karita, S., Wakagi, T., Shoun, H., Watanabe, T., Fushinobu, S.

(2010) FEBS Lett 584: 1205-1211

• PubMed: 20159017 
• DOI: 10.1016/j.febslet.2010.02.027
• Primary Citation of Related Structures:  
  3ACF, 3ACG, 3ACH, 3ACI


• PubMed Abstract: 
  

The crystal structures of a carbohydrate-binding module (CBM) family 28 domain of endoglucanase Cel5A from Clostridium josui have been determined in ligand-free and complex forms with cellobiose, cellotetraose, and cellopentaose as the first complex structures of this family. In the cleft of a beta-sandwich fold, the ligands are recognized by stacking interactions and hydrogen bonds. Conformations of the bound cellooligosaccharides are similar to those in crystals and solution but clearly different from the cellulose structure. Interestingly, the glucan chain bound on CBM28 is in the opposite direction of that bound to CBM17, although these families share significant structural similarity.

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Organizational Affiliation: 

Department of Biotechnology, The University of Tokyo, Tokyo, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-1,4-endoglucanase	A	203	Ruminiclostridium josui	Mutation(s): 0  Gene Names: celA EC: 3.2.1.4
UniProt
Find proteins for Q59290 (Ruminiclostridium josui) Explore Q59290  Go to UniProtKB:  Q59290

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	B	4		N/A
Glycosylation Resources
GlyTouCan:  G00025MO GlyCosmos:  G00025MO GlyGen:  G00025MO

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900011	B	beta-cellotetraose	Oligosaccharide / Metabolism		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.198 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.576	α = 90
b = 63.9	β = 90
c = 75.619	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-01-04 
• Released Date: 2010-03-02 
Deposition Author(s): Tsukimoto, K., Takada, R., Araki, Y., Suzuki, K., Karita, S., Wakagi, T., Shoun, H., Watanabe, T., Fushinobu, S.

Revision History  

• Version 1.0: 2010-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-10-30
  Changes: Database references
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary