9UDP | pdb_00009udp

Single-chain Fv antibody of B2

• PDB DOI: https://doi.org/10.2210/pdb9UDP/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-04-07 Released: 2025-11-05 
• Deposition Author(s): Yoshida, M., Hanazono, Y., Numoto, N., Ito, N., Oda, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.174 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Structural basis of anti-(4-hydroxy-3-nitrophenyl)acetyl antibodies during affinity maturation

Yoshida, M., Hanazono, Y., Numoto, N., Yabuno, S., Ito, N., Azuma, T., Oda, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 26.22 kDa 
• Atom Count: 2,167 
• Modeled Residue Count: 229 
• Deposited Residue Count: 245 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Single-chain Fv antibody of B2	A	245	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	B [auth A], C [auth A], D [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.174 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.762	α = 90
b = 71.956	β = 90
c = 81.289	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Yoshida, M., Hanazono, Y., Numoto, N., Ito, N., Oda, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release