6FWG

Structure of an E333Q variant of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with tetramannoside yeast mannan fragment

• PDB DOI: https://doi.org/10.2210/pdb6FWG/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides xylanisolvens XB1A
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-03-06 Released: 2019-09-18 
• Deposition Author(s): Sobala, L.F., Speciale, G., Hakki, Z., Fernandes, P.Z., Raich, L., Rojas-Cervellera, V., Bennet, A., Thompson, A.J., Bernardo-Seisdedos, G., Millet, O., Zhu, S., Lu, D., Sollogoub, M., Rovira, C., Jimenez-Barbero, J., Davies, G.J., Williams, S.J.
• Funding Organization(s): European Research Council, Australian Research Council, Spanish Ministry of Economy and Competitiveness, Agency for Administration of University and Research, Generalitat de Catalunya

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.07 Å
• R-Value Free: 0.138 
• R-Value Work: 0.120 
• R-Value Observed: 0.121 

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 44.73 kDa 
• Atom Count: 3,465 
• Modelled Residue Count: 346 
• Deposited Residue Count: 385 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolase family 71	A	385	Bacteroides xylanisolvens XB1A	Mutation(s): 1  Gene Names: BXY_34140
UniProt
Find proteins for D6D1V7 (Bacteroides xylanisolvens XB1A) Explore D6D1V7  Go to UniProtKB:  D6D1V7

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-methyl alpha-D-mannopyranoside	B	4		N/A
Glycosylation Resources
GlyTouCan:  G71057YG GlyCosmos:  G71057YG

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth A], D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.07 Å
• R-Value Free: 0.138 
• R-Value Work: 0.120 
• R-Value Observed: 0.121 
• Space Group: I 4
• Diffraction Data: https://doi.org/10.5281/zenodo.4424526

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.873	α = 90
b = 107.873	β = 90
c = 67.626	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-18 
Deposition Author(s): Sobala, L.F., Speciale, G., Hakki, Z., Fernandes, P.Z., Raich, L., Rojas-Cervellera, V., Bennet, A., Thompson, A.J., Bernardo-Seisdedos, G., Millet, O., Zhu, S., Lu, D., Sollogoub, M., Rovira, C., Jimenez-Barbero, J., Davies, G.J., Williams, S.J.

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Funding Organization	Location	Grant Number
European Research Council	United Kingdom	322942
Australian Research Council	Australia	FT130100103
Australian Research Council	Australia	DP120101396
Spanish Ministry of Economy and Competitiveness	Spain	CTQ2017-85496-P
Spanish Ministry of Economy and Competitiveness	Spain	CTQ2015-64597-C2-1P
Agency for Administration of University and Research	Spain	2017SGR-1189
Generalitat de Catalunya	Spain	2014SGR-987

Revision History  

• Version 1.0: 2019-09-18
  Type: Initial release
  
• Version 1.1: 2020-06-10
  Changes: Data collection, Database references
• Version 1.2: 2020-07-08
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2021-02-03
  Changes: Database references, Structure summary
• Version 2.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description