3OMB | pdb_00003omb

Crystal structure of extracellular solute-binding protein from Bifidobacterium longum subsp. infantis

• PDB DOI: https://doi.org/10.2210/pdb3OMB/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: 2010-08-26 Released: 2010-09-08 
• Deposition Author(s): Chang, C., Xu, X., Chin, S., Cui, H., Dong, A., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Literature

Crystal structure of extracellular solute-binding protein from Bifidobacterium longum subsp. infantis

Chang, C., Xu, X., Chin, S., Cui, H., Dong, A., Savchenko, A., Edwards, A., Joachimiak, A.

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)

Macromolecule Content 

• Total Structure Weight: 59.86 kDa 
• Atom Count: 4,396 
• Modeled Residue Count: 503 
• Deposited Residue Count: 535 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular solute-binding protein, family 1	A	535	Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088	Mutation(s): 0  Gene Names: Blon_2351
UniProt
Find proteins for B7GNQ3 (Bifidobacterium longum subsp. infantis (strain ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12)) Explore B7GNQ3  Go to UniProtKB:  B7GNQ3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
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: 2.10 Å
• R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.949	α = 90
b = 70.099	β = 90
c = 122.177	γ = 90

Software Package:

Software Name	Purpose
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
MLPHARE	phasing
DM	phasing
RESOLVE	phasing
Coot	model building
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-08 
Deposition Author(s): Chang, C., Xu, X., Chin, S., Cui, H., Dong, A., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-09-08
  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