5D9M

Crystal structure of PbGH5A, a glycoside hydrolase family 5 enzyme from Prevotella bryantii B14, E280A mutant in complex with the xyloglucan tetradecasaccharide XXXGXXXG

• PDB DOI: https://doi.org/10.2210/pdb5D9M/pdb

• Classification: HYDROLASE
• Organism(s): Segatella bryantii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-08-18 Released: 2015-11-04 
• Deposition Author(s): Morar, M., Stogios, P.J., Xu, X., Cui, H., Di Leo, R., Yim, V., Savchenko, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.204 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 81.83 kDa 
• Atom Count: 6,442 
• Modelled Residue Count: 693 
• Deposited Residue Count: 706 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B-1,4-endoglucanase	A, B	353	Segatella bryantii	Mutation(s): 1
UniProt
Find proteins for O06842 (Segatella bryantii) Explore O06842  Go to UniProtKB:  O06842

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C	7		N/A
Glycosylation Resources
GlyTouCan:  G53479JR GlyCosmos:  G53479JR

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose	D	14		N/A
Glycosylation Resources
GlyTouCan:  G16324DM GlyCosmos:  G16324DM

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.204 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.431	α = 90
b = 81.677	β = 90
c = 108.492	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-04 
Deposition Author(s): Morar, M., Stogios, P.J., Xu, X., Cui, H., Di Leo, R., Yim, V., Savchenko, A.

Revision History  

• Version 1.0: 2015-11-04
  Type: Initial release
  
• Version 1.1: 2015-11-11
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary