6VRT | pdb_00006vrt

LT1009 humanized antibody Fab fragment in complex with calcium

• PDB DOI: https://doi.org/10.2210/pdb6VRT/pdb

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


• Deposited: 2020-02-09 Released: 2020-04-29 
• Deposition Author(s): Fleming, J.K., Huxford, T.
• Funding Organization(s): National Science Foundation (United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free: 
  0.260 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Ion binding properties of a naturally occurring metalloantibody

Farokhi, E., Fleming, J.K., Erasmus, M.F., Ward, A.D., Wu, Y., Gutierrez, M.G., Wojciak, J.M., Huxford, T.

(2020) Antibodies (Basel) 9: 10

• DOI: https://doi.org/10.3390/antib9020010

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: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 48.05 kDa 
• Atom Count: 3,397 
• Modeled Residue Count: 439 
• Deposited Residue Count: 439 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sonepcizumab antibody Fab fragment, heavy chain	A [auth H]	225	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sonepcizumab antibody Fab fragment, light chain	B [auth L]	214	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth H]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	D [auth L], E [auth L]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free:  0.260 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.802	α = 90
b = 114.408	β = 90
c = 133.702	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-04-29 
Deposition Author(s): Fleming, J.K., Huxford, T.

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Funding Organization	Location	Grant Number
National Science Foundation (United States)	United States	CHE-1112547

Revision History  

• Version 1.0: 2020-04-29
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary