Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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: 60.59 kDa 
• Atom Count: 4892 
• Modelled Residue Count: 555 
• Deposited Residue Count: 555 
• Unique protein chains: 3

1YQV

The crystal structure of the antibody Fab HyHEL5 complex with lysozyme at 1.7A resolution

• PDB DOI: 10.2210/pdb1YQV/pdb
• Entry: 1YQV supersedes: 3HFL

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Gallus gallus
• Mutation(s): No 


• Deposited: 2005-02-02 Released: 2005-04-26 
• Deposition Author(s): Cohen, G.H., Silverton, E.W., Padlan, E.A., Dyda, F., Wibbenmeyer, J.A., Wilson, R.C., Davies, D.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.234 
• R-Value Work: 0.195 

Literature

Water molecules in the antibody-antigen interface of the structure of the Fab HyHEL-5-lysozyme complex at 1.7 A resolution: comparison with results from isothermal titration calorimetry.

Cohen, G.H., Silverton, E.W., Padlan, E.A., Dyda, F., Wibbenmeyer, J.A., Willson, R.C., Davies, D.R.

(2005) Acta Crystallogr D Biol Crystallogr 61: 628-633

• PubMed: 15858274 
• DOI: 10.1107/S0907444905007870
• Primary Citation of Related Structures:  
  1YQV


• PubMed Abstract: 
  

The structure of the complex between hen egg-white lysozyme and the Fab HyHEL-5 at 2.7 A resolution has previously been reported [Cohen et al. (1996), Acta Cryst. D52, 315-326]. With the availability of recombinant Fab, the X-ray structure of the complex has been re-evaluated at 1.7 A resolution. The refined structure has yielded a detailed picture of the Fab-lysozyme interface, showing the high complementarity of the protein surfaces as well as several water molecules within the interface that complete the good fit. The model of the full complex has improved significantly, yielding an R(work) of 19.5%. With this model, the structural results can be compared with the results of isothermal titration calorimetry. An attempt has been made to estimate the changes in bound waters that accompany complex formation and the difficulties inherent in using the crystal structures to provide the information necessary to make this calculation are discussed.

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Organizational Affiliation: 

National Institutes of Health, 5 Center Drive, MSC 0560, Bethesda, MD 20892-0560, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HyHEL-5 Antibody Light Chain	A [auth L]	211	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HyHEL-5 Antibody Heavy Chain	B [auth H]	215	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hen Egg White Lysozyme	C [auth Y]	129	Gallus gallus	Mutation(s): 0  Gene Names: LYZ 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: 1.70 Å
• R-Value Free: 0.234 
• R-Value Work: 0.195 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.459	α = 90
b = 74.258	β = 101.65
c = 78.256	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
X-PLOR	model building
CNS	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-02-02 
• Released Date: 2005-04-26 
Deposition Author(s): Cohen, G.H., Silverton, E.W., Padlan, E.A., Dyda, F., Wibbenmeyer, J.A., Wilson, R.C., Davies, D.R.
• This entry supersedes: 3HFL

Revision History  

• Version 1.0: 2005-04-26
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description