6D5B

Structure of Caldicellulosiruptor danielii CBM3 module of glycoside hydrolase WP_045175321

• PDB DOI: https://doi.org/10.2210/pdb6D5B/pdb

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


• Deposited: 2018-04-19 Released: 2019-04-24 
• Deposition Author(s): Alahuhta, P.M., Lunin, V.V.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.243 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 

Literature

Novel multidomain, multifunctional glycoside hydrolases from highly lignocellulolytic Caldicellulosiruptor species

Conway, J.M., Crosby, J.R., Hren, A.P., Southerland, R.T., Lee, L.L., Lunin, V.V., Alahuhta, P.M., Himmel, M.E., Bomble, Y.J., Adams, M.W.W., Kelly, R.M.

(2019) AIChE J 

• DOI: https://doi.org/10.1002/aic.16354

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Biological Assembly 7  

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

Biological assembly 7 assigned by authors.

Biological Assembly 8  

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

Biological assembly 8 assigned by authors.

Biological Assembly 9  

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

Biological assembly 9 assigned by authors.

Biological Assembly 10  

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

Biological assembly 10 assigned by authors.

Biological Assembly 11  

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

Biological assembly 11 assigned by authors.

Biological Assembly 12  

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

Biological assembly 12 assigned by authors.

Macromolecule Content

• Total Structure Weight: 227.99 kDa 
• Atom Count: 16,774 
• Modelled Residue Count: 1,835 
• Deposited Residue Count: 2,040 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glycoside hydrolase WP_045175321	A, B, C, D, E, F, G, H, I, J, K, L	170	Caldicellulosiruptor danielii	Mutation(s): 0  EC: 3.2.1
UniProt
Find proteins for A0A4V8GZQ7 (Caldicellulosiruptor danielii) Explore A0A4V8GZQ7  Go to UniProtKB:  A0A4V8GZQ7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	M [auth A], N [auth B], O [auth C], P [auth D], Q [auth E], R [auth F], S [auth G], T [auth H], U [auth I], V [auth J], W [auth K], X [auth L]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.243 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.167	α = 83.87
b = 86.199	β = 83.93
c = 86.567	γ = 60.55

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-04-24 
Deposition Author(s): Alahuhta, P.M., Lunin, V.V.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	--

Revision History  

• Version 1.0: 2019-04-24
  Type: Initial release
  
• Version 1.1: 2019-06-05
  Changes: Data collection, Database references
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description