3T3A

Crystal structure of H107R mutant of extracellular domain of mouse receptor NKR-P1A

• PDB DOI: https://doi.org/10.2210/pdb3T3A/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-07-25 Released: 2011-08-10 
• Deposition Author(s): Kolenko, P., Rozbesky, D., Bezouska, K., Hasek, J., Dohnalek, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.216 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 

Starting Model: experimental

Literature

Structure of the H107R variant of the extracellular domain of mouse NKR-P1A at 2.3 A resolution.

Kolenko, P., Rozbesky, D., Vanek, O., Bezouska, K., Hasek, J., Dohnalek, J.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1519-1523

• PubMed: 22139156 
• DOI: https://doi.org/10.1107/S1744309111046203
• Primary Citation of Related Structures:  
  3T3A


• PubMed Abstract: 
  

  The structure of the H107R variant of the extracellular domain of the mouse natural killer cell receptor NKR-P1A has been determined by X-ray diffraction at 2.3 Å resolution from a merohedrally twinned crystal. Unlike the structure of the wild-type receptor in space group I4(1)22 with a single chain per asymmetric unit, the crystals of the variant belonged to space group I4(1) with a dimer in the asymmetric unit. Different degrees of merohedral twinning were detected in five data sets collected from different crystals. The mutation does not have a significant impact on the overall structure, but led to the binding of an additional phosphate ion at the interface of the molecules.

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Organizational Affiliation: 

Institute of Macromolecular Chemistry AS CR, vvi, Prague, Czech Republic. [e-mail]

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: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 32.34 kDa 
• Atom Count: 2,016 
• Modelled Residue Count: 241 
• Deposited Residue Count: 278 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Killer cell lectin-like receptor subfamily B member 1A	A, B	139	Mus musculus	Mutation(s): 3  Gene Names: Klrb1a, Ly55, Ly55a, Nkrp1a
UniProt
Find proteins for P27811 (Mus musculus) Explore P27811  Go to UniProtKB:  P27811

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth A], E [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.216 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 
• Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.741	α = 90
b = 64.741	β = 90
c = 156.096	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-10 
Deposition Author(s): Kolenko, P., Rozbesky, D., Bezouska, K., Hasek, J., Dohnalek, J.

Revision History  

• Version 1.0: 2011-08-10
  Type: Initial release
  
• Version 1.1: 2011-12-14
  Changes: Database references
• Version 1.2: 2012-03-28
  Changes: Database references
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description