1ZPL

E. coli F17a-G lectin domain complex with GlcNAc(beta1-O)Me


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Impact of natural variation in bacterial F17G adhesins on crystallization behaviour.

Buts, L.Wellens, A.Van Molle, I.Wyns, L.Loris, R.Lahmann, M.Oscarson, S.De Greve, H.Bouckaert, J.

(2005) Acta Crystallogr D Biol Crystallogr 61: 1149-1159

  • DOI: https://doi.org/10.1107/S0907444905017038
  • Primary Citation of Related Structures:  
    1ZK5, 1ZPL, 2BS7, 2BS8, 2BSB, 2BSC

  • PubMed Abstract: 

    Since the introduction of structural genomics, the protein has been recognized as the most important variable in crystallization. Recent strategies to modify a protein to improve crystal quality have included rationally engineered point mutations, truncations, deletions and fusions. Five naturally occurring variants, differing in 1-18 amino acids, of the 177-residue lectin domain of the F17G fimbrial adhesin were expressed and purified in identical ways. For four out of the five variants crystals were obtained, mostly in non-isomorphous space groups, with diffraction limits ranging between 2.4 and 1.1 A resolution. A comparative analysis of the crystal-packing contacts revealed that the variable amino acids are often involved in lattice contacts and a single amino-acid substitution can suffice to radically change crystal packing. A statistical approach proved reliable to estimate the compatibilities of the variant sequences with the observed crystal forms. In conclusion, natural variation, universally present within prokaryotic species, is a valuable genetic resource that can be favourably employed to enhance the crystallization success rate with considerably less effort than other strategies.


  • Organizational Affiliation

    Laboratorium voor Ultrastructuur, Vlaams Interuniversitair Instituut voor Biotechnologie and Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
F17a-G
A, B
177Escherichia coliMutation(s): 0 
Gene Names: F17G AF022140
UniProt
Find proteins for Q99003 (Escherichia coli)
Explore Q99003 
Go to UniProtKB:  Q99003
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99003
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MAG
Query on MAG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside
C9 H17 N O6
ZEVOCXOZYFLVKN-JGKVKWKGSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.212 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.805α = 90
b = 42.805β = 90
c = 288.244γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-23
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-10-05
    Changes: Derived calculations
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2023-08-23
    Changes: Data collection, Database references, Refinement description, Structure summary