8DOZ

Protective antibody against gonococcal lipooligosaccharide

• PDB DOI: https://doi.org/10.2210/pdb8DOZ/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2022-07-14 Released: 2023-06-21 
• Deposition Author(s): Beernink, P.T.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.216 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 

Literature

Protective antibody against gonococcal lipooligosaccharide bound to a peptide mimetic vaccine antigen

Beernink, P.T., Ram, S.

(null) Tbd 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 93.57 kDa 
• Atom Count: 6,903 
• Modelled Residue Count: 839 
• Deposited Residue Count: 872 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 2C7, heavy chain Fd fragment	A, C	221	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 2C7 lambda light chain	B, D	215	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	E [auth A], H [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.216 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40	α = 92.13
b = 50.61	β = 86.78
c = 106.21	γ = 82.26

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-21 
Deposition Author(s): Beernink, P.T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI134868

Revision History  

• Version 1.0: 2023-06-21
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description