2XFW | pdb_00002xfw

Structure of the E192N mutant of E. coli N-acetylneuraminic acid lyase in complex with pyruvate in crystal form III

• PDB DOI: https://doi.org/10.2210/pdb2XFW/pdb

• Classification: LYASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-05-28 Released: 2010-09-22 
• Deposition Author(s): Campeotto, I., Murshudov, G.N., Bolt, A.H., Trinh, C.H., Phillips, S.E.V., Nelson, A., Pearson, A.R., Berry, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.182 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Structural Insights Into Substrate Specificity in Variants of N-Acetylneuraminic Acid Lyase Produced by Directed Evolution.

Campeotto, I., Bolt, A.H., Harman, T.A., Dennis, C., Trinh, C.H., Phillips, S.E.V., Nelson, A., Pearson, A.R., Berry, A.

To be published.

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: 136.04 kDa 
• Atom Count: 10,447 
• Modeled Residue Count: 1,195 
• Deposited Residue Count: 1,216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-ACETYLNEURAMINIC ACID LYASE	A, B, C, D	304	Escherichia coli	Mutation(s): 1  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	F [auth A], G [auth A], M [auth D], N [auth D]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PYR	E [auth A], H [auth B], I [auth C], J [auth C], K [auth C], L [auth D]	PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KPI	A, B, C, D	L-PEPTIDE LINKING	C9 H16 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.182 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.11	α = 90
b = 116.53	β = 117.95
c = 83.74	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-22 
Deposition Author(s): Campeotto, I., Murshudov, G.N., Bolt, A.H., Trinh, C.H., Phillips, S.E.V., Nelson, A., Pearson, A.R., Berry, A.

Revision History  

• Version 1.0: 2010-09-22
  Type: Initial release
  
• Version 1.1: 2013-03-13
  Changes: Structure summary
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations, Other
• Version 2.1: 2023-11-29
  Changes: Data collection
• Version 2.2: 2023-12-20
  Changes: Refinement description