1J05 | pdb_00001j05

The crystal structure of anti-carcinoembryonic antigen monoclonal antibody T84.66 Fv fragment

• PDB DOI: https://doi.org/10.2210/pdb1J05/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-11-01 Released: 2003-12-16 
• Deposition Author(s): Kondo, H., Nishimura, Y., Shiroishi, M., Asano, R., Noro, N., Tsumoto, K., Kumagai, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.217 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

The crystal structure of anti-carcinoembryonic antigen monoclonal antibody T84.66 Fv fragment

Kondo, H., Nishimura, Y., Shiroishi, M., Asano, R., Noro, N., Tsumoto, K., Kumagai, I.

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 and generated by PISA (software)

Biological Assembly 2  

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 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 51.07 kDa 
• Atom Count: 3,859 
• Modeled Residue Count: 464 
• Deposited Residue Count: 464 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-CEA mAb T84.66, light chain	A [auth L], C [auth A]	111	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01660 (Mus musculus) Explore P01660  Go to UniProtKB:  P01660

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-CEA mAb T84.66, heavy chain	B [auth H], D [auth B]	121	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q9JL85 (Mus musculus) Explore Q9JL85  Go to UniProtKB:  Q9JL85

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	F [auth H], H [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	E [auth L], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.217 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.774	α = 90
b = 75.033	β = 94.82
c = 63.105	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CNS	refinement
SHELXL-97	refinement
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-12-16 
Deposition Author(s): Kondo, H., Nishimura, Y., Shiroishi, M., Asano, R., Noro, N., Tsumoto, K., Kumagai, I.

Revision History  

• Version 1.0: 2003-12-16
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-10-23
  Changes: Structure summary