1K53

Monomeric Protein L B1 Domain with a G15A Mutation

• PDB DOI:  https://doi.org/10.2210/pdb1K53/pdb

• Classification: PROTEIN BINDING
• Organism(s): Finegoldia magna ATCC 29328
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2001-10-09 Released: 2001-12-05 
• Deposition Author(s): O'Neill, J.W., Kim, D.E., Johnsen, K., Baker, D., Zhang, K.Y.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.233 
• R-Value Work: 0.213 
• R-Value Observed: 0.230 

Literature

Single-site mutations induce 3D domain swapping in the B1 domain of protein L from Peptostreptococcus magnus.

O'Neill, J.W., Kim, D.E., Johnsen, K., Baker, D., Zhang, K.Y.

(2001) Structure 9: 1017-1027

• PubMed: 11709166 
• DOI: https://doi.org/10.1016/s0969-2126(01)00667-0
• Primary Citation of Related Structures:  
  1K50, 1K51, 1K52, 1K53


• PubMed Abstract: 
  

Thermodynamic and kinetic studies of the Protein L B1 domain (Ppl) suggest a folding pathway in which, during the folding transition, the first beta hairpin is formed while the second beta hairpin and the alpha helix are largely unstructured. The same mutations in the two beta turns have opposite effects on the folding and unfolding rates. Three of the four residues composing the second beta turn in Ppl have consecutive positive phi angles, indicating strain in the second beta turn.

---

Organizational Affiliation: 

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 16.66 kDa 
• Atom Count: 1,282 
• Modelled Residue Count: 144 
• Deposited Residue Count: 144 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein L	A, B	72	Finegoldia magna ATCC 29328	Mutation(s): 2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.233 
• R-Value Work: 0.213 
• R-Value Observed: 0.230 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.511	α = 90
b = 66.511	β = 90
c = 109.192	γ = 120

Software Package:

Software Name	Purpose
EPMR	phasing
CNS	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-12-05 
Deposition Author(s): O'Neill, J.W., Kim, D.E., Johnsen, K., Baker, D., Zhang, K.Y.J.

Revision History  

• Version 1.0: 2001-12-05
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations, Refinement description
• Version 1.4: 2023-08-16
  Changes: Data collection, Refinement description