3PH6 | pdb_00003ph6

Bovine beta lactoglobulin crytsallized through ligandation of yttrium

• PDB DOI: https://doi.org/10.2210/pdb3PH6/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2010-11-03 Released: 2011-09-21 
• Deposition Author(s): Zocher, G., Stehle, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free: 
  0.265 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.216 (Depositor) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

Novel Approach to Protein Crystallization through Ligandation of Yttrium Cations

Zhang, F., Zocher, G., Sauter, A., Stehle, T., Schreiber, F.

(2011) J Appl Crystallogr 44: 755-762

• DOI: https://doi.org/10.1107/S0021889811017997

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: 36.8 kDa 
• Atom Count: 2,505 
• Modeled Residue Count: 317 
• Deposited Residue Count: 322 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactoglobulin	A, B	161	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P02754 (Bos taurus) Explore P02754  Go to UniProtKB:  P02754

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YT3	C [auth A], D [auth A], G [auth B], H [auth B]	YTTRIUM (III) ION Y GRTBAGCGDOYUBE-UHFFFAOYSA-N
CL	E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free:  0.265 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.216 (Depositor) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.06	α = 90
b = 63.71	β = 90
c = 134.16	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-21 
Deposition Author(s): Zocher, G., Stehle, T.

Revision History  

• Version 1.0: 2011-09-21
  Type: Initial release
  
• Version 1.1: 2014-02-19
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2020-01-15
  Changes: Data collection
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary