4PI7 | pdb_00004pi7

Crystal structure of S. Aureus Autolysin E in complex with disaccharide NAM-NAG

• PDB DOI: https://doi.org/10.2210/pdb4PI7/pdb

• Classification: HYDROLASE
• Organism(s): Staphylococcus aureus subsp. aureus Mu50
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-05-08 Released: 2015-10-14 
• Deposition Author(s): Mihelic, M., Renko, M., Jakas, A., Turk, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.187 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Literature

The mechanism behind the selection of two different cleavage sites in NAG-NAM polymers

Mihelic, M., Vlahovicek-Kahlina, K., Renko, M., Mesnage, S., Dobersek, A., Taler-Vercic, A., Jakas, A., Turk, D.

(2017) IUCrJ 4: 185-198

• DOI: https://doi.org/10.1107/S2052252517000367

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 27.05 kDa 
• Atom Count: 2,110 
• Modelled Residue Count: 223 
• Deposited Residue Count: 228 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Autolysin E	A	228	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0  Gene Names: SAV2307
UniProt
Find proteins for A0A0H3JT72 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore A0A0H3JT72  Go to UniProtKB:  A0A0H3JT72

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid	B	2		N/A
Glycosylation Resources
GlyTouCan:  G99515FY GlyCosmos:  G99515FY

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	N [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.187 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.31	α = 90
b = 69.782	β = 90
c = 73.58	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-14 
Deposition Author(s): Mihelic, M., Renko, M., Jakas, A., Turk, D.

Revision History  

• Version 1.0: 2015-10-14
  Type: Initial release
  
• Version 1.1: 2017-03-08
  Changes: Database references
• Version 1.2: 2017-09-27
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-12-27
  Changes: Data collection, Database references, Derived calculations, Structure summary