5O2N

Lytic transglycosylase in action

• PDB DOI: https://doi.org/10.2210/pdb5O2N/pdb
• Entry: 5O2N supersedes: 4YP4

• Classification: HYDROLASE
• Organism(s): Neisseria meningitidis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2017-05-22 Released: 2018-03-14 
• Deposition Author(s): Williams, A.H., Hoauz, A., Boneca, I.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free: 0.192 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 4YP4

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 69.77 kDa 
• Atom Count: 5,648 
• Modelled Residue Count: 577 
• Deposited Residue Count: 616 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transglycosylase	A	616	Neisseria meningitidis	Mutation(s): 0  Gene Names: slt, ERS514729_01258 EC: 4.2.2
UniProt
Find proteins for Q9JXP1 (Neisseria meningitidis serogroup B (strain MC58)) Explore Q9JXP1  Go to UniProtKB:  Q9JXP1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose	B	4		N/A
Glycosylation Resources
GlyTouCan:  G93613RO GlyCosmos:  G93613RO GlyGen:  G93613RO

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
FLC	D [auth A]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free: 0.192 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.1	α = 90
b = 72.6	β = 90
c = 125	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-03-14 
Deposition Author(s): Williams, A.H., Hoauz, A., Boneca, I.G.
• This entry supersedes: 4YP4

Revision History  

• Version 1.0: 2018-03-14
  Type: Initial release
  
• Version 1.1: 2018-05-02
  Changes: Data collection, Database references
• Version 1.2: 2018-11-28
  Changes: Data collection, Structure summary
• Version 1.3: 2019-10-16
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary