1FDL

CRYSTALLOGRAPHIC REFINEMENT OF THE THREE-DIMENSIONAL STRUCTURE OF THE FAB D1.3-LYSOZYME COMPLEX AT 2.5-ANGSTROMS RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1FDL/pdb

• Classification: COMPLEX (ANTIBODY-ANTIGEN)
• Organism(s): Mus musculus, Gallus gallus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1990-08-27 Released: 1991-10-15 
• Deposition Author(s): Fischmann, T.O., Poljak, R.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.184 

Literature

Crystallographic refinement of the three-dimensional structure of the FabD1.3-lysozyme complex at 2.5-A resolution.

Fischmann, T.O., Bentley, G.A., Bhat, T.N., Boulot, G., Mariuzza, R.A., Phillips, S.E., Tello, D., Poljak, R.J.

(1991) J Biol Chem 266: 12915-12920

• PubMed: 1712773 
• Primary Citation of Related Structures:  
  1FDL


• PubMed Abstract: 
  

  The three-dimensional crystal structure of the complex between the Fab from the monoclonal anti-lysozyme antibody D1.3 and the antigen, hen egg white lysozyme, has been refined by crystallographic techniques using x-ray intensity data to 2.5-A resolution. The antibody contacts the antigen with residues from all its complementarity determining regions. Antigen residues 18-27 and 117-125 form a discontinuous antigenic determinant making hydrogen bonds and van der Waals interactions with the antibody. Water molecules at or near the antigen-antibody interface mediate some contacts between antigen and antibody. The fine specificity of antibody D1.3, which does not bind (K alpha less than 10(5) M-1) avian lysozymes where Gln121 in the amino acid sequence is occupied by His, can be explained on the basis of the refined model.

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Organizational Affiliation: 

Département d'Immunologie, Institut Pasteur, Paris, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 61.41 kDa 
• Atom Count: 4,309 
• Modelled Residue Count: 561 
• Deposited Residue Count: 561 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IGG1-KAPPA D1.3 FAB (LIGHT CHAIN)	A [auth L]	214	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01837 (Mus musculus) Explore P01837  Go to UniProtKB:  P01837

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IGG1-KAPPA D1.3 FAB (HEAVY CHAIN)	B [auth H]	218	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01868 (Mus musculus) Explore P01868  Go to UniProtKB:  P01868

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HEN EGG WHITE LYSOZYME	C [auth Y]	129	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.184 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56	α = 90
b = 143.5	β = 120.4
c = 49.3	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1991-10-15 
Deposition Author(s): Fischmann, T.O., Poljak, R.J.

Revision History  

• Version 1.0: 1991-10-15
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.4: 2024-11-20
  Changes: Structure summary