6D2Y | pdb_00006d2y

Crystal structure of surface glycan-binding protein PbSGBP-B from Prevotella bryantii

• PDB DOI: https://doi.org/10.2210/pdb6D2Y/pdb

• Classification: SUGAR BINDING PROTEIN
• 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., Wawrzak, Z., 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: 2.19 Å
• R-Value Free: 
  0.240 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Crystal structure of surface glycan-binding protein PbSGBP-B 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: 51.82 kDa 
• Atom Count: 3,531 
• Modeled Residue Count: 428 
• Deposited Residue Count: 460 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PbSGBP-B lipoprotein	A	460	Segatella baroniae B14	Mutation(s): 0  Gene Names: PBR_0365
UniProt
Find proteins for D8DY16 (Segatella baroniae B14) Explore D8DY16  Go to UniProtKB:  D8DY16

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.240 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.9	α = 90
b = 82.9	β = 90
c = 152.47	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	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., Wawrzak, Z., 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: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary