8P2T | pdb_00008p2t

Bovine naive ultralong antibody AbD08* collected at 100K

• PDB DOI: https://doi.org/10.2210/pdb8P2T/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Bos taurus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-05-16 Released: 2024-07-10 
• Deposition Author(s): Clarke, J.D., Douangamath, A., Mikolajek, H., Stuart, D.I., Owens, R.J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Models: experimental

Literature

The impact of chain-exchange on bovine ultralong immunoglobulins.

Clarke, J.D., Douangamath, A., Mikolajek, H., Placido, M.B.D., Stuart, D.I., Hammond, J., Owens, R.J.

(2024) Acta Crystallographica Section F 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 57.5 kDa 
• Atom Count: 4,132 
• Modeled Residue Count: 483 
• Deposited Residue Count: 546 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody D08* heavy chain	A [auth H]	307	Bos taurus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody D08* light chain	B [auth L]	239	Bos taurus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRD	D [auth H]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
NA	C [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.03	α = 90
b = 70.86	β = 90
c = 96.01	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
pointless	data scaling
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-10 
Deposition Author(s): Clarke, J.D., Douangamath, A., Mikolajek, H., Stuart, D.I., Owens, R.J.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/M011224/1

Revision History  

• Version 1.0: 2024-07-10
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Structure summary