3P6B | pdb_00003p6b

The crystal structure of CelK CBM4 from Clostridium thermocellum

• PDB DOI: https://doi.org/10.2210/pdb3P6B/pdb

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


• Deposited: 2010-10-11 Released: 2011-08-24 
• Deposition Author(s): Alahuhta, P.M., Luo, Y., Lunin, V.V.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.274 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Structure of CBM4 from Clostridium thermocellum cellulase K.

Alahuhta, M., Luo, Y., Ding, S.Y., Himmel, M.E., Lunin, V.V.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 527-530

• PubMed: 21543854 
• DOI: https://doi.org/10.1107/S1744309111003307
• Primary Citation Related Structures: 
  3P6B


• PubMed Abstract: 
  

  Here, a 2.0 Å resolution X-ray structure of Clostridium thermocellum cellulase K family 4 carbohydrate-binding module (CelK CBM4) is reported. The resulting structure was refined to an R factor of 0.212 and an R(free) of 0.274. Structural analysis shows that this new structure is very similar to the previously solved structure of C. thermocellum CbhA CBM4. Most importantly, these data support the previously proposed notion of an extended binding pocket using a novel tryptophan-containing loop that may be highly conserved in clostridial CBM4 proteins.

---

Organizational Affiliation: 
• BioSciences Center, National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, Colorado 80401-3305, USA.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.46 kDa 
• Atom Count: 3,474 
• Modeled Residue Count: 372 
• Deposited Residue Count: 410 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellulose 1,4-beta-cellobiosidase	A, B	205	Acetivibrio thermocellus	Mutation(s): 0  Gene Names: celK EC: 3.2.1.91
UniProt
Find proteins for P0C2S1 (Acetivibrio thermocellus) Explore P0C2S1  Go to UniProtKB:  P0C2S1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	H [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth A], M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	D [auth A], E [auth A], F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	C [auth A], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.274 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.949	α = 90
b = 65.949	β = 90
c = 272.436	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
MOLREP	phasing
REFMAC	refinement
SAINT	data reduction
PROTEUM PLUS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-24 
Deposition Author(s): Alahuhta, P.M., Luo, Y., Lunin, V.V.

Revision History  

• Version 1.0: 2011-08-24
  Type: Initial release
  
• Version 1.1: 2013-03-27
  Changes: Other
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description