9GP2 | pdb_00009gp2

apoJ22.9 Unliganded structure of an Fab fragment from the therapeutic antibody J22.9-xi

• PDB DOI: https://doi.org/10.2210/pdb9GP2/pdb

• Classification: ANTITUMOR PROTEIN
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-09-06 Released: 2024-09-25 
• Deposition Author(s): Marino, S.F., Daumke, O.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.202 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

apoJ22.9 Unliganded structure of an Fab fragment from the therapeutic antibody J22.9-xi

Marino, S.F., Daumke, O.

To be published.

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.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 47.26 kDa 
• Atom Count: 3,918 
• Modeled Residue Count: 435 
• Deposited Residue Count: 435 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chains: H	A [auth H]	222	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Chains: L	B [auth L]	213	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.202 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.374	α = 90
b = 122.374	β = 90
c = 170.125	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-09-25 
Deposition Author(s): Marino, S.F., Daumke, O.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-09-25
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Structure summary