5OFS | pdb_00005ofs

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 (Depositor), 0.151 (DCC) 
  • R-Value Work: 
    0.125 (Depositor), 0.134 (DCC) 
  • R-Value Observed: 
    0.126 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5OFS

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 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.

Macromolecule Content 

  • Total Structure Weight: 26.89 kDa 
  • Atom Count: 2,176 
  • Modeled Residue Count: 224 
  • Deposited Residue Count: 224 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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

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 (Depositor), 0.151 (DCC) 
  • R-Value Work:  0.125 (Depositor), 0.134 (DCC) 
  • R-Value Observed: 0.126 (Depositor) 
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