Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 49.21 kDa 
• Atom Count: 3405 
• Modelled Residue Count: 411 
• Deposited Residue Count: 447 
• Unique protein chains: 2

1MJ7

Crystal Structure Of The Complex Of The Fab fragment of Esterolytic Antibody MS5-393 and A Transition-State Analog

• PDB DOI: 10.2210/pdb1MJ7/pdb

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


• Deposited: 2002-08-27 Released: 2003-09-23 
• Deposition Author(s): Ruzheinikov, S.N., Muranova, T.A., Sedelnikova, S.E., Partridge, L.J., Blackburn, G.M., Murray, I.A., Kakinuma, H., Takashi, N., Shimazaki, K., Sun, J., Nishi, Y., Rice, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.303 
• R-Value Work: 0.200 

Literature

High-resolution crystal structure of the Fab-fragments of a family of mouse catalytic antibodies with esterase activity

Ruzheinikov, S.N., Muranova, T.A., Sedelnikova, S.E., Partridge, L.J., Blackburn, G.M., Murray, I.A., Kakinuma, H., Takashi, N., Shimazaki, K., Sun, J., Nishi, Y., Rice, D.W.

(2003) J Mol Biol 332: 423-435

• PubMed: 12948492 
• DOI: 10.1016/s0022-2836(03)00902-1
• Primary Citation of Related Structures:  
  1MH5, 1MIE, 1MJ7, 1MJ8, 1MJJ, 1MJU


• PubMed Abstract: 
  

The crystal structures of four related Fab fragments of a family of catalytic antibodies displaying differential levels of esterase activity have been solved in the presence and in the absence of the transition-state analogue (TSA) that was used to elicit the immune response. The electron density maps show that the TSA conformation is essentially identical, with limited changes on hapten binding. Interactions with the TSA explain the specificity for the D rather than the L-isomer of the substrate. Differences in the residues in the hapten-binding pocket, which increase hydrophobicity, appear to correlate with an increase in the affinity of the antibodies for their substrate. Analysis of the structures at the active site reveals a network of conserved hydrogen bond contacts between the TSA and the antibodies, and points to a critical role of two conserved residues, HisL91 and LysH95, in catalysis. However, these two key residues are set into very different contexts in their respective structures, with an apparent direct correlation between the catalytic power of the antibodies and the complexity of their interactions with the rest of the protein. This suggests that the catalytic efficiency may be controlled by contacts arising from a second sphere of residues at the periphery of the active site.

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Related Citations: 

• The preparation and crystallization of Fab fragments of a family of mouse esterolytic catalytic antibodies and their complexes with a transition-state analogue
  Muranova, T.A., Ruzheinikov, S.N., Sedelnikova, S.E., Moir, A., Partridge, L.J., Kakinuma, H., Takashi, N., Shimazaki, K., Sun, J., Nishi, Y., Rice, D.W.
  (2001) Acta Crystallogr D Biol Crystallogr 57: 1192

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Organizational Affiliation: 

Krebs Institute for Biomolecular Research, University of Sheffield, Firth Court, Western Bank, S10 2TN Sheffield, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IMMUNOGLOBULIN MS5-393	A [auth L]	219	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IMMUNOGLOBULIN MS5-393	B [auth H]	228	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HAL	C [auth H]	N-{[2-({[1-(4-CARBOXYBUTANOYL)AMINO]-2-PHENYLETHYL}-HYDROXYPHOSPHINYL)OXY]ACETYL}-2-PHENYLETHYLAMINE C23 H29 N2 O7 P DKQZZKSBRCTCQU-QFIPXVFZSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
HAL	Binding MOAD:  1MJ7	Kd: 4.5 (nM) from 1 assay(s)
	PDBBind:  1MJ7	Kd: 4.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.303 
• R-Value Work: 0.200 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.237	α = 90
b = 40.531	β = 109.72
c = 85.903	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-08-27 
• Released Date: 2003-09-23 
Deposition Author(s): Ruzheinikov, S.N., Muranova, T.A., Sedelnikova, S.E., Partridge, L.J., Blackburn, G.M., Murray, I.A., Kakinuma, H., Takashi, N., Shimazaki, K., Sun, J., Nishi, Y., Rice, D.W.

Revision History  

• Version 1.0: 2003-09-23
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model