5OFS

X-ray structure of a zinc binding GB1 mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.126 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Genetic Algorithm Based Design and Experimental Characterization of a Highly Thermostable Metalloprotein.

Bozkurt, E.Perez, M.A.S.Hovius, R.Browning, N.J.Rothlisberger, U.

(2018) J Am Chem Soc 140: 4517-4521

  • DOI: https://doi.org/10.1021/jacs.7b10660
  • Primary Citation of Related Structures:  
    5O94, 5OFS

  • PubMed Abstract: 

    The development of thermostable and solvent-tolerant metalloproteins is a long-sought goal for many applications in synthetic biology and biotechnology. In this work, we were able to engineer a highly thermostable and organic solvent-stable metallo variant of the B1 domain of protein G (GB1) with a tetrahedral zinc binding site reminiscent of the one of thermolysin. Promising candidates were designed computationally by applying a protocol based on classical and first-principles molecular dynamics simulations in combination with genetic algorithm optimization. The most promising of the computationally predicted mutants was expressed and structurally characterized and yielded a highly thermostable protein. The experimental results thus confirm the predictive power of the applied computational protein engineering approach for the de novo design of highly stable metalloproteins.


  • Organizational Affiliation

    Laboratory of Computational Chemistry and Biochemistry , École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne , Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Immunoglobulin G-binding protein G
A, B, C, D
56Streptococcus sp. 'group GMutation(s): 0 
Gene Names: spg
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MRD
Query on MRD

Download Ideal Coordinates CCD File 
Q [auth D](4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
K [auth B],
M [auth C]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
T [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
J [auth B]
L [auth C]
O [auth D]
E [auth A],
F [auth A],
J [auth B],
L [auth C],
O [auth D],
P [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
I [auth A],
N [auth C],
V [auth D],
W [auth D],
X [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
U [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

Download Ideal Coordinates CCD File 
R [auth D],
S [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.126 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.452α = 90
b = 75.621β = 90
c = 51.153γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADDREFdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland200020-146645

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-04
    Type: Initial release
  • Version 1.1: 2018-04-11
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary