6YHQ | pdb_00006yhq

Crystal Structure of Fab F5.18.6, anti-Plasmodium vivax AMA1

• PDB DOI: https://doi.org/10.2210/pdb6YHQ/pdb

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


• Deposited: 2020-03-30 Released: 2021-04-14 
• Deposition Author(s): Bentley, G.A., Saul, F.A., Vulliez-le Normand, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.239 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Models: experimental

Literature

Crystal Structure of Fab F5.18.6, anti-Plasmodium vivax AMA1

Bentley, G.A., Saul, F.A., Vulliez-le Normand, B.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 46.6 kDa 
• Atom Count: 3,652 
• Modeled Residue Count: 423 
• Deposited Residue Count: 432 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab F5.18.6 anti-Plasmodium vivax AMA1, heavy chain	A [auth H]	220	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab F5.18.6 anti-Plasmodium vivax AMA1, kappa light chain	B [auth L]	212	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
SCN	D [auth L]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	B [auth L]	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.239 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.08	α = 90
b = 114.99	β = 90
c = 40.68	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-14 
Deposition Author(s): Bentley, G.A., Saul, F.A., Vulliez-le Normand, B.

Revision History  

• Version 1.0: 2021-04-14
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary