Biological Assembly 1  

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

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 25.27 kDa 
• Atom Count: 2068 
• Modelled Residue Count: 228 
• Deposited Residue Count: 228 
• Unique protein chains: 1

1QAC

CHANGE IN DIMERIZATION MODE BY REMOVAL OF A SINGLE UNSATISFIED POLAR RESIDUE

• PDB DOI: 10.2210/pdb1QAC/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-02-25 Released: 2000-02-23 
• Deposition Author(s): Pokkuluri, P.R., Cai, X., Johnson, G., Stevens, F.J., Schiffer, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.226 
• R-Value Work: 0.193 

Literature

Change in dimerization mode by removal of a single unsatisfied polar residue located at the interface.

Pokkuluri, P.R., Cai, X., Johnson, G., Stevens, F.J., Schiffer, M.

(2000) Protein Sci 9: 1852-1855

• PubMed: 11045631 
• DOI: 10.1110/ps.9.9.1852
• Primary Citation of Related Structures:  
  1QAC, 5LVE


• PubMed Abstract: 
  

The importance of unsatisfied hydrogen bonding potential on protein-protein interaction was studied. Two alternate modes of dimerization (conventional and flipped form) of an immunoglobulin light chain variable domain (V(L)) were previously identified. In the flipped form, interface residue Gln89 would have an unsatisfied hydrogen bonding potential. Removal of this Gln should render the flipped dimer as the more favorable quaternary form. High resolution crystallographic studies of the Q89A and Q89L mutants show, as we predicted, that these proteins indeed form flipped dimers with very similar interfaces. A small cavity is present in the Q89A mutant that is reflected in the approximately 100 times lower association constant than found for the Q89L mutant. The association constant of Q89A and Q89L proteins (4 x 10(6) M(-1) and >10(8) M(-1)) are 10- and 1,000-fold higher than that of the wild-type protein that forms conventional dimers clearly showing the energetic reasons for the flipped dimer formation.

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Related Citations: 

• A domain flip as a result of a single amino-acid substitution.
  Pokkuluri, P.R., Huang, D.-B., Raffen, R., Cai, X., Johnson, G., Wilkins Stevens, P., Stevens, F.J., Schiffer, M.
  (1998) Structure 6: 1067

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Organizational Affiliation: 

Argonne National Laboratory, Biosciences Division, Illinois 60439, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IMMUNOGLOBULIN LIGHT CHAIN VARIABLE DOMAIN	A, B	114	Homo sapiens	Mutation(s): 0  Gene Names: IGKV4-1
UniProt & NIH Common Fund Data Resources
Find proteins for P06312 (Homo sapiens) Explore P06312  Go to UniProtKB:  P06312
PHAROS:  P06312

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.226 
• R-Value Work: 0.193 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.3	α = 90
b = 83.6	β = 109
c = 42.8	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-02-25 
• Released Date: 2000-02-23 
Deposition Author(s): Pokkuluri, P.R., Cai, X., Johnson, G., Stevens, F.J., Schiffer, M.

Revision History  

• Version 1.0: 2000-02-23
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description