1OF3 | pdb_00001of3

Structural and thermodynamic dissection of specific mannan recognition by a carbohydrate-binding module, TmCBM27

• PDB DOI: https://doi.org/10.2210/pdb1OF3/pdb

• Classification: HYDROLASE/CARBOHYDRATE BINDING
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2003-04-07 Released: 2003-04-17 
• Deposition Author(s): Boraston, A.B., Revett, T.J., Boraston, C.M., Nurizzo, D., Davies, G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.225 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

Structural and Thermodynamic Dissection of Specific Mannan Recognition by a Carbohydrate Binding Module, Tmcbm27

Boraston, A.B., Revett, T.J., Boraston, C.M., Nurizzo, D., Davies, G.J.

(2003) Structure 11: 665

• PubMed: 12791255 
• DOI: https://doi.org/10.1016/s0969-2126(03)00100-x
• Primary Citation Related Structures: 
  1OF3, 1OF4, 1OH4


• PubMed Abstract: 
  

  The C-terminal 176 amino acids of a Thermotoga maritima mannanase (Man5) constitute a carbohydrate binding module (CBM) that has been classified into CBM family 27. The isolated CBM27 domain, named TmCBM27, binds tightly (K(a)s 10(5)-10(6) M(-1)) to beta-1, 4-mannooligosaccharides, carob galactomannan, and konjac glucomannan, but not to cellulose (insoluble and soluble) or soluble birchwood xylan. The X-ray crystal structures of native TmCBM27, a TmCBM27-mannohexaose complex, and a TmCBM27-6(3),6(4)-alpha-D-galactosyl-mannopentaose complex at 2.0 A, 1.6 A, and 1.35 A, respectively, reveal the basis of TmCBM27's specificity for mannans. In particular, the latter complex, which is the first structure of a CBM in complex with a branched plant cell wall polysaccharide, illustrates how the architecture of the binding site can influence the recognition of naturally substituted polysaccharides.

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Organizational Affiliation: 
• Department of Chemistry, University of York, Heslington, York YO10 5YW, 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: 41.34 kDa 
• Atom Count: 3,130 
• Modeled Residue Count: 350 
• Deposited Residue Count: 358 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-MANNOSIDASE	A, B	179	Thermotoga maritima MSB8	Mutation(s): 0  EC: 3.2.1.78
UniProt
Find proteins for Q9RIK9 (Thermotoga maritima) Explore Q9RIK9  Go to UniProtKB:  Q9RIK9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.225 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.078	α = 90
b = 69.078	β = 90
c = 229.474	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-04-17 
Deposition Author(s): Boraston, A.B., Revett, T.J., Boraston, C.M., Nurizzo, D., Davies, G.J.

Revision History  

• Version 1.0: 2003-04-17
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary