3QDE | pdb_00003qde

The structure of Cellobiose phosphorylase from Clostridium thermocellum in complex with phosphate

• PDB DOI: https://doi.org/10.2210/pdb3QDE/pdb

• Classification: TRANSFERASE
• Organism(s): Acetivibrio thermocellus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-01-18 Released: 2011-11-09 
• Deposition Author(s): Bianchetti, C.M., Elsen, N.L., Horn, M.K., Fox, B.G., Phillips Jr., G.N.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.208 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Literature

Structure of cellobiose phosphorylase from Clostridium thermocellum in complex with phosphate.

Bianchetti, C.M., Elsen, N.L., Fox, B.G., Phillips, G.N.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1345-1349

• PubMed: 22102229 
• DOI: https://doi.org/10.1107/S1744309111032660
• Primary Citation Related Structures: 
  3QDE


• PubMed Abstract: 
  

  Clostridium thermocellum is a cellulosome-producing bacterium that is able to efficiently degrade and utilize cellulose as a sole carbon source. Cellobiose phosphorylase (CBP) plays a critical role in cellulose degradation by catalyzing the reversible phosphate-dependent hydrolysis of cellobiose, the major product of cellulose degradation, into α-D-glucose 1-phosphate and D-glucose. CBP from C. thermocellum is a modular enzyme composed of four domains [N-terminal domain, helical linker, (α/α)(6)-barrel domain and C-terminal domain] and is a member of glycoside hydrolase family 94. The 2.4 Å resolution X-ray crystal structure of C. thermocellum CBP reveals the residues involved in coordinating the catalytic phosphate as well as the residues that are likely to be involved in substrate binding and discrimination.

---

Organizational Affiliation: 
• Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 186.41 kDa 
• Atom Count: 13,881 
• Modeled Residue Count: 1,622 
• Deposited Residue Count: 1,622 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellobiose phosphorylase	A, B	811	Acetivibrio thermocellus	Mutation(s): 0  Gene Names: cbp, Q8VP44 EC: 2.4.1.20
UniProt
Find proteins for Q8VP44 (Acetivibrio thermocellus) Explore Q8VP44  Go to UniProtKB:  Q8VP44

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
144	D [auth A], F [auth B]	TRIS-HYDROXYMETHYL-METHYL-AMMONIUM C4 H12 N O3 DRDCQJADRSJFFD-UHFFFAOYSA-N
PO4	C [auth A], E [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.208 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.262	α = 90
b = 122.062	β = 90
c = 181.996	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-09 
Deposition Author(s): Bianchetti, C.M., Elsen, N.L., Horn, M.K., Fox, B.G., Phillips Jr., G.N.

Revision History  

• Version 1.0: 2011-11-09
  Type: Initial release
  
• Version 1.1: 2012-04-11
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Advisory, Refinement description
• Version 1.3: 2024-02-21
  Changes: Advisory, Data collection, Database references, Derived calculations