2APF

Crystal Structure of the A52V/S54N/K66E variant of the murine T cell receptor V beta 8.2 domain

• PDB DOI: https://doi.org/10.2210/pdb2APF/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-08-16 Released: 2006-03-21 
• Deposition Author(s): Cho, S., Swaminathan, C.P., Yang, J., Kerzic, M.C., Guan, R., Kieke, M.C., Kranz, D.M., Mariuzza, R.A., Sundberg, E.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.263 
• R-Value Work: 0.197 
• R-Value Observed: 0.201 

Literature

Structural basis of affinity maturation and intramolecular cooperativity in a protein-protein interaction.

Cho, S., Swaminathan, C.P., Yang, J., Kerzic, M.C., Guan, R., Kieke, M.C., Kranz, D.M., Mariuzza, R.A., Sundberg, E.J.

(2005) Structure 13: 1775-1787

• PubMed: 16338399 
• DOI: https://doi.org/10.1016/j.str.2005.11.001
• Primary Citation of Related Structures:  
  2APB, 2APF, 2APT, 2APV, 2APW, 2APX, 2AQ1, 2AQ2, 2AQ3

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.32 kDa 
• Atom Count: 1,018 
• Modelled Residue Count: 112 
• Deposited Residue Count: 112 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor beta chain V	A	112	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for A2NAI0 (Rattus norvegicus) Explore A2NAI0  Go to UniProtKB:  A2NAI0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLA	B [auth A]	MALONIC ACID C3 H4 O4 OFOBLEOULBTSOW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.263 
• R-Value Work: 0.197 
• R-Value Observed: 0.201 
• Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.608	α = 90
b = 74.708	β = 90
c = 113.819	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
d*TREK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-21 
Deposition Author(s): Cho, S., Swaminathan, C.P., Yang, J., Kerzic, M.C., Guan, R., Kieke, M.C., Kranz, D.M., Mariuzza, R.A., Sundberg, E.J.

Revision History  

• Version 1.0: 2006-03-21
  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: 2015-04-29
  Changes: Non-polymer description
• Version 1.4: 2018-04-04
  Changes: Data collection
• Version 1.5: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary