6GMM | pdb_00006gmm

Crystal structure of Helicobacter pylori adhesin LabA

• PDB DOI: https://doi.org/10.2210/pdb6GMM/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-05-27 Released: 2019-12-18 
• Deposition Author(s): Paraskevopoulou, V., Overman, R.C., Stolnik, S., Winkler, S., Gellert, P., Falcone, F.H., Schimpl, M.
• Funding Organization(s): Engineering and Physical Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 
  0.252 (Depositor), 0.293 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Structural and binding characterization of the LacdiNAc-specific adhesin (LabA; HopD) exodomain from Helicobacter pylori

Paraskevopoulou, V., Schimpl, M., Overman, R.C., Stolnik, S., Chen, Y., Nguyen, L., Winkler, G.S., Gellert, P., Klassen, J.S., Falcone, F.H.

(2021) Current Research In Structural Biology 

• DOI: https://doi.org/10.1016/j.crstbi.2020.12.004

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 48.79 kDa 
• Atom Count: 3,402 
• Modeled Residue Count: 433 
• Deposited Residue Count: 455 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
adhesin LabA	A	455	Helicobacter pylori	Mutation(s): 0  Gene Names: BW246_00440, BZL55_00170

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free:  0.252 (Depositor), 0.293 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.86	α = 90
b = 59.86	β = 90
c = 264.74	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
STARANISO	data scaling
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-12-18 
Deposition Author(s): Paraskevopoulou, V., Overman, R.C., Stolnik, S., Winkler, S., Gellert, P., Falcone, F.H., Schimpl, M.

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Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	EP/L01646X

Revision History  

• Version 1.0: 2019-12-18
  Type: Initial release
  
• Version 1.1: 2020-12-30
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary