3QUF | pdb_00003quf

The structure of a family 1 extracellular solute-binding protein from Bifidobacterium longum subsp. infantis

• PDB DOI: https://doi.org/10.2210/pdb3QUF/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-02-23 Released: 2011-05-04 
• Deposition Author(s): Cuff, M.E., Xu, X., Cui, H., Chin, S., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.180 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Literature

The structure of a family 1 extracellular solute-binding protein from Bifidobacterium longum subsp. infantis

Cuff, M.E., Xu, X., Cui, H., Chin, S., Savchenko, A., Edwards, A., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 92.07 kDa 
• Atom Count: 6,979 
• Modeled Residue Count: 775 
• Deposited Residue Count: 828 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular solute-binding protein, family 1	A, B	414	Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088	Mutation(s): 0  Gene Names: Blon_0375
UniProt
Find proteins for B7GMZ0 (Bifidobacterium longum subsp. infantis (strain ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12)) Explore B7GMZ0  Go to UniProtKB:  B7GMZ0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], F [auth B], H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACY	E [auth A], G [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.180 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.532	α = 90
b = 105.095	β = 90
c = 145.375	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-04 
Deposition Author(s): Cuff, M.E., Xu, X., Cui, H., Chin, S., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2011-05-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary