5O2O | pdb_00005o2o

Lytic transglycosylase in action

• PDB DOI: https://doi.org/10.2210/pdb5O2O/pdb

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


• Deposited: 2017-05-22 Released: 2018-06-13 
• Deposition Author(s): Williams, A.H., Hoauz, A., Boneca, I.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free: 
  0.226 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Lytic transglycosylase in action

Williams, A.H., Wheeler, R., Rateau, L., Malosse, C., Rooke, J.C., Hoauz, A., Taha, M.-K., Boneca, I.G.

To be published.

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: 68.87 kDa 
• Atom Count: 5,423 
• Modeled Residue Count: 576 
• 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 ATCC BAA-335 / MC58)) Explore Q9JXP1  Go to UniProtKB:  Q9JXP1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NHE	C [auth A], D [auth A], E [auth A]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free:  0.226 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.714	α = 90
b = 72.681	β = 90
c = 124.924	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-06-13 
Deposition Author(s): Williams, A.H., Hoauz, A., Boneca, I.G.

Revision History  

• Version 1.0: 2018-06-13
  Type: Initial release
  
• Version 1.1: 2018-11-28
  Changes: Data collection, Structure summary
• Version 1.2: 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
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-09
  Changes: Structure summary