5DQJ | pdb_00005dqj

Structure of unliganded S55-5 Fab

• PDB DOI: https://doi.org/10.2210/pdb5DQJ/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2015-09-14 Released: 2016-03-09 
• Deposition Author(s): Haji-Ghassemi, O., Evans, S.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Lipid A-antibody structures reveal a widely-utilized pocket specific for negatively charged groups derived from unrelated V-genes

Haji-Ghassemi, O., Muller-Loennies, S., Rodriguez, T., Brade, L., Kosma, P., Brade, H., Evans, S.V.

(2015) J Biological Chem 

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 2  

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

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

Macromolecule Content 

• Total Structure Weight: 95.87 kDa 
• Atom Count: 6,772 
• Modeled Residue Count: 878 
• Deposited Residue Count: 880 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S55-5 Fab (IgG1 kappa) light chain	A [auth L], C [auth B]	218	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S55-5 Fab (IgG1) heavy chain	B [auth H], D [auth A]	222	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.607	α = 90
b = 139.872	β = 110.66
c = 72.076	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-09 
Deposition Author(s): Haji-Ghassemi, O., Evans, S.V.

Revision History  

• Version 1.0: 2016-03-09
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary