8CC3 | pdb_00008cc3

Vibrio cholerae GbpA (LPMO domain)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 
    0.201 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.183 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8CC3

This is version 1.1 of the entry. See complete history

Literature

Perdeuterated GbpA Enables Neutron Scattering Experiments of a Lytic Polysaccharide Monooxygenase.

Sorensen, H.V.Montserrat-Canals, M.Loose, J.S.M.Fisher, S.Z.Moulin, M.Blakeley, M.P.Cordara, G.Bjerregaard-Andersen, K.Krengel, U.

(2023) ACS Omega 8: 29101-29112

  • DOI: https://doi.org/10.1021/acsomega.3c02168
  • Primary Citation Related Structures: 
    8CC3, 8CC5

  • PubMed Abstract: 

    Lytic polysaccharide monooxygenases (LPMOs) are surface-active redox enzymes that catalyze the degradation of recalcitrant polysaccharides, making them important tools for energy production from renewable sources. In addition, LPMOs are important virulence factors for fungi, bacteria, and viruses. However, many knowledge gaps still exist regarding their catalytic mechanism and interaction with their insoluble, crystalline substrates. Moreover, conventional structural biology techniques, such as X-ray crystallography, usually do not reveal the protonation state of catalytically important residues. In contrast, neutron crystallography is highly suited to obtain this information, albeit with significant sample volume requirements and challenges associated with hydrogen's large incoherent scattering signal. We set out to demonstrate the feasibility of neutron-based techniques for LPMOs using N -acetylglucosamine-binding protein A (GbpA) from Vibrio cholerae as a target. GbpA is a multifunctional protein that is secreted by the bacteria to colonize and degrade chitin. We developed an efficient deuteration protocol, which yields >10 mg of pure 97% deuterated protein per liter expression media, which was scaled up further at international facilities. The deuterated protein retains its catalytic activity and structure, as demonstrated by small-angle X-ray and neutron scattering studies of full-length GbpA and X-ray crystal structures of its LPMO domain (to 1.1 Å resolution), setting the stage for neutron scattering experiments with its substrate chitin.


  • Organizational Affiliation
    • Department of Chemistry, University of Oslo, NO-0315 Oslo, Norway.

Macromolecule Content 

  • Total Structure Weight: 40.37 kDa 
  • Atom Count: 3,526 
  • Modeled Residue Count: 360 
  • Deposited Residue Count: 360 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GlcNAc-binding protein A
A, B
180Vibrio cholerae O1 biovar El TorMutation(s): 0 
Gene Names: gbpAVCA0811
UniProt
Find proteins for Q9KLD5 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9KLD5 
Go to UniProtKB:  Q9KLD5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KLD5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
I [auth A]
K [auth B]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
(Subject of Investigation/LOI)

Query on CU



Download:Ideal Coordinates CCD File
E [auth A],
J [auth B]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
N [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free:  0.201 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.183 (DCC) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.911α = 90
b = 89.103β = 90
c = 47.135γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Norwegian Research CouncilNorway272201
Norwegian Research CouncilNorway245828

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-30
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Structure summary