2YGY | pdb_00002ygy

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

• PDB DOI: https://doi.org/10.2210/pdb2YGY/pdb

• Classification: LYASE
• Organism(s): Escherichia coli BL21(DE3)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-04-23 Released: 2012-04-04 
• Deposition Author(s): Campeotto, I., Nelson, A., Berry, A., Phillips, S.E.V., Pearson, A.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.224 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

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

• PubMed: 30291262 
• DOI: https://doi.org/10.1038/s41598-018-32962-6
• Primary Citation Related Structures: 
  2YGY


• 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 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.

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Organizational Affiliation: 
• Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK. [e-mail].
Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 1HY, UK. [e-mail].
Leicester Institute of Structural and Chemical Biology, University of Leicester, Lancaster Road, Leicester, LE1 7RH, UK. [e-mail].
Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxford, OX11 OFA, UK.
Department of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 1HY, UK.
Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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. [e-mail].
Hamburg Centre for Ultrafast Imaging, Institute of Nanostructure and Solid State Physics, Universität Hamburg, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 134.96 kDa 
• Atom Count: 9,923 
• Modeled Residue Count: 1,189 
• Deposited Residue Count: 1,216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-ACETYLNEURAMINATE LYASE	A, B, C, D	304	Escherichia coli BL21(DE3)	Mutation(s): 0  EC: 4.1.3.3
UniProt
Find proteins for P0A6L4 (Escherichia coli (strain K12)) Explore P0A6L4  Go to UniProtKB:  P0A6L4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	G [auth B], I [auth C]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
CL	E [auth A], F [auth B], H [auth C], J [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.224 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.26	α = 90
b = 95.87	β = 115.33
c = 91.38	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-04 
Deposition Author(s): Campeotto, I., Nelson, A., Berry, A., Phillips, S.E.V., Pearson, A.R.

Revision History  

• Version 1.0: 2012-04-04
  Type: Initial release
  
• Version 1.1: 2018-10-17
  Changes: Data collection, Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description