1YUP

Reindeer beta-lactoglobulin

• PDB DOI: https://doi.org/10.2210/pdb1YUP/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Rangifer tarandus
• Mutation(s): No 


• Deposited: 2005-02-14 Released: 2006-02-14 
• Deposition Author(s): Goldman, A., Oksanen, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.311 
• R-Value Work: 0.235 
• R-Value Observed: 0.239 

Starting Model: experimental

Literature

Reindeer beta-lactoglobulin crystal structure with pseudo-body-centred noncrystallographic symmetry.

Oksanen, E., Jaakola, V.P., Tolonen, T., Valkonen, K., Akerstrom, B., Kalkkinen, N., Virtanen, V., Goldman, A.

(2006) Acta Crystallogr D Biol Crystallogr 62: 1369-1374

• PubMed: 17057340 
• DOI: https://doi.org/10.1107/S0907444906031519
• Primary Citation of Related Structures:  
  1YUP


• PubMed Abstract: 
  

  Reindeer beta-lactoglobulin (betaLG) belongs to the lipocalin superfamily. Its DNA and protein sequences have been determined and showed that it had nine residue changes from bovine betaLG. Reindeer betaLG, the structure of which was finally determined at 2.1 A resolution in space group P1, crystallized in a unit cell that is both P2-like and P2(1)-like owing to the presence of an almost perfect (but noncrystallographic) body-centring vector. The non-body-centred data could only be observed using a very bright synchrotron beam and a novel refinement strategy was adopted to enable us to use the weak h + k + l = 2n + 1 reflections.

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Organizational Affiliation: 

Institute of Biotechnology, University of Helsinki, Finland.

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 146.37 kDa 
• Atom Count: 10,045 
• Modelled Residue Count: 1,263 
• Deposited Residue Count: 1,296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-lactoglobulin	A, B, C, D, E, F, G, H	162	Rangifer tarandus	Mutation(s): 0
UniProt
Find proteins for Q00P86 (Rangifer tarandus tarandus) Explore Q00P86  Go to UniProtKB:  Q00P86

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.311 
• R-Value Work: 0.235 
• R-Value Observed: 0.239 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.24	α = 90
b = 94.14	β = 105.76
c = 64.15	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ProDC	data collection
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-02-14 
Deposition Author(s): Goldman, A., Oksanen, E.

Revision History  

• Version 1.0: 2006-02-14
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-11-20
  Changes: Structure summary