7VFR | pdb_00007vfr

GltA N83K mutant from Bifidobacterium infantis JCM 1222 complexed with lacto-N-tetraose

• PDB DOI: https://doi.org/10.2210/pdb7VFR/pdb

• Classification: TRANSLOCASE
• Organism(s): Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-09-13 Released: 2022-09-14 
• Deposition Author(s): Sato, M., Sakanaka, M., Katayama, T., Fushinobu, S.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

Short stretch sequence of a milk oligosaccharide transporter represents the phenotypic selection trajectory in infant gut microbiome

Sakanaka, M., Sato, M., Fushinobu, S., Katayama, T.

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: 44.81 kDa 
• Atom Count: 3,448 
• Modeled Residue Count: 397 
• Deposited Residue Count: 411 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular solute-binding protein, family 1	A	411	Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088	Mutation(s): 1  Gene Names: Blon_2177
UniProt
Find proteins for B7GN82 (Bifidobacterium longum subsp. infantis (strain ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12)) Explore B7GN82  Go to UniProtKB:  B7GN82

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	B	4		N/A
Glycosylation Resources
GlyTouCan:  G00049MO GlyCosmos:  G00049MO GlyGen:  G00049MO

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.995	α = 107.05
b = 42.39	β = 102.06
c = 59.605	γ = 104.29

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-09-14 
Deposition Author(s): Sato, M., Sakanaka, M., Katayama, T., Fushinobu, S.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18K14379
Japan Society for the Promotion of Science (JSPS)	Japan	17K19231
Japan Society for the Promotion of Science (JSPS)	Japan	21H02116

Revision History  

• Version 1.0: 2022-09-14
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description