4NLI | pdb_00004nli

Crystal structure of sheep beta-lactoglobulin (space group P3121)

• PDB DOI: https://doi.org/10.2210/pdb4NLI/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Ovis aries
• Mutation(s): No 


• Deposited: 2013-11-14 Released: 2014-03-12 
• Deposition Author(s): Loch, J.I., Molenda, M., Kopec, M., Swiatek, S., Lewinski, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.206 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.201 (DCC) 

Starting Model: experimental

Literature

Structure of two crystal forms of sheep beta-lactoglobulin with EF-loop in closed conformation

Loch, J.I., Molenda, M., Kopec, M., Swiatek, S., Lewinski, K.

(2014) Biopolymers 101: 886-894

• PubMed: 25098178 
• DOI: https://doi.org/10.1002/bip.22471
• Primary Citation Related Structures: 
  4NLI, 4NLJ


• PubMed Abstract: 
  

  Ovine β-lactoglobulin has been isolated from whey fraction of sheep milk and crystallized. The high-resolution structures of two crystal forms (triclinic and trigonal) obtained at pH 7.0 have been determined revealing that ovine protein, similarly to its bovine analog, is dimeric. Access to the binding site located in the eight-stranded antiparallel β-barrel in both structures is blocked by the EF loop that has been found in closed conformation. Similarly to bovine lactoglobulin (BLG), conformation of the EF loop is stabilized by hydrogen bond between Glu89 and Ser116 indicating that Tanford transition might occur with the same mechanism. The substitution at six positions in relation to the most abundant isoform B of BLG also affects the distribution of electrostatic potentials and the total charge.

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Organizational Affiliation: 
• Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry Jagiellonian University in Kraków, Ingardena 3, Kraków, 30-060, Poland.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 18.58 kDa 
• Atom Count: 1,531 
• Modeled Residue Count: 162 
• Deposited Residue Count: 162 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactoglobulin-1/B	A	162	Ovis aries	Mutation(s): 0
UniProt
Find proteins for P67976 (Ovis aries) Explore P67976  Go to UniProtKB:  P67976

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.206 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.201 (DCC) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.44	α = 90
b = 97.44	β = 90
c = 68.24	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-12 
Deposition Author(s): Loch, J.I., Molenda, M., Kopec, M., Swiatek, S., Lewinski, K.

Revision History  

• Version 1.0: 2014-03-12
  Type: Initial release
  
• Version 1.1: 2014-03-19
  Changes: Database references, Derived calculations
• Version 1.2: 2014-12-10
  Changes: Database references
• Version 1.3: 2017-11-22
  Changes: Data collection, Refinement description
• Version 1.4: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-30
  Changes: Structure summary