2YGY

Structure of wild type E. coli N-acetylneuraminic acid lyase in space group P21 crystal form II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Pathological macromolecular crystallographic data affected by twinning, partial-disorder and exhibiting multiple lattices for testing of data processing and refinement tools.

Campeotto, I.Lebedev, A.Schreurs, A.M.M.Kroon-Batenburg, L.M.J.Lowe, E.Phillips, S.E.V.Murshudov, G.N.Pearson, A.R.

(2018) Sci Rep 8: 14876-14876

  • DOI: 10.1038/s41598-018-32962-6

  • PubMed Abstract: 
  • Twinning is a crystal growth anomaly, which has posed a challenge in macromolecular crystallography (MX) since the earliest days. Many approaches have been used to treat twinned data in order to extract structural information. However, in most cases ...

    Twinning is a crystal growth anomaly, which has posed a challenge in macromolecular crystallography (MX) since the earliest days. Many approaches have been used to treat twinned data in order to extract structural information. However, in most cases it is usually simpler to rescreen for new crystallization conditions that yield an untwinned crystal form or, if possible, collect data from non-twinned parts of the crystal. Here, we report 11 structures of engineered variants of the E. coli enzyme N-acetyl-neuraminic lyase which, despite twinning and incommensurate modulation, have been successfully indexed, solved and deposited. These structures span a resolution range of 1.45-2.30 Å, which is unusually high for datasets presenting such lattice disorders in MX and therefore these data provide an excellent test set for improving and challenging MX data processing programs.


    Organizational Affiliation

    Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 1HY, UK. ivan.campeotto@leicester.ac.uk.,Department of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK. ivan.campeotto@leicester.ac.uk.,Leicester Institute of Structural and Chemical Biology, University of Leicester, Lancaster Road, Leicester, LE1 7RH, UK. ivan.campeotto@leicester.ac.uk.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxford, OX11 OFA, UK.,Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 1HY, UK.,Hamburg Centre for Ultrafast Imaging, Institute of Nanostructure and Solid State Physics, Universität Hamburg, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany. arwen.pearson@cfel.de.,Structural Studies Division, MRC-LMB, Francis Crick Avenue, Cambridge, CB2 0QH, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK. arwen.pearson@cfel.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-ACETYLNEURAMINATE LYASE
A, B, C, D
304Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: nanA (npl)
EC: 4.1.3.3
Find proteins for P0A6L4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6L4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
1PE
Query on 1PE

Download SDF File 
Download CCD File 
B, C
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 84.260α = 90.00
b = 95.870β = 115.33
c = 91.380γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-04
    Type: Initial release
  • Version 1.1: 2018-10-17
    Type: Data collection, Database references