6D2W | pdb_00006d2w

Crystal structure of Prevotella bryantii endo-beta-mannanase/endo-beta-glucanase PbGH26A-GH5A

• PDB DOI: https://doi.org/10.2210/pdb6D2W/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., Nocek, B., 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: 2.10 Å
• R-Value Free: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Models: experimental

Literature

Crystal structure of Prevotella bryantii endo-beta-mannanase/endo-beta-glucanase PbGH26A-GH5A

McGregor, N.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 174.99 kDa 
• Atom Count: 12,730 
• Modelled Residue Count: 1,372 
• Deposited Residue Count: 1,552 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aryl-phospho-beta-D-glucosidase BglC, GH1 family	A, B	776	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	E [auth A], F [auth A], H [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
GOL	C [auth A], D [auth A], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.484	α = 90
b = 96.753	β = 99.27
c = 138.089	γ = 90

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., Nocek, B., 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