6D2X | pdb_00006d2x

Crystal structure of the GH26 domain from PbGH26-GH5A endo-beta-mannanase/endo-beta-glucanase from Prevotella bryantii

• PDB DOI: https://doi.org/10.2210/pdb6D2X/pdb

• Classification: HYDROLASE
• Organism(s): Segatella baroniae B14
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-04-14 Released: 2019-10-16 
• Deposition Author(s): Stogios, P.J., Skarina, T., McGregor, N., Di Leo, R., Brumer, H., Savchenko, A.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the GH26 domain from PbGH26-GH5A endo-beta-mannanase/endo-beta-glucanase from Prevotella bryantii

McGregor, N.

To be published.

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: 41.7 kDa 
• Atom Count: 3,354 
• Modeled Residue Count: 336 
• Deposited Residue Count: 337 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aryl-phospho-beta-D-glucosidase BglC, GH1 family	A	337	Segatella baroniae B14	Mutation(s): 0  Gene Names: PBR_0368, SAMN05444375_1266
UniProt
Find proteins for D8DY19 (Segatella baroniae B14) Explore D8DY19  Go to UniProtKB:  D8DY19

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE3	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL C28 H58 O15 ILLKMACMBHTSHP-UHFFFAOYSA-N
SO4	H [auth A], I [auth A], J [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.577	α = 90
b = 73.577	β = 90
c = 105.086	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-10-16 
Deposition Author(s): Stogios, P.J., Skarina, T., McGregor, N., Di Leo, R., Brumer, H., Savchenko, A.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	Industrial Biocatalysis Network

Revision History  

• Version 1.0: 2019-10-16
  Type: Initial release
  
• Version 1.1: 2020-01-08
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description