5LEO | pdb_00005leo

Complex structure of lysostaphin SH3b domain with peptidoglycan fragment

• PDB DOI: https://doi.org/10.2210/pdb5LEO/pdb

• Classification: CELL ADHESION
• Organism(s): Staphylococcaceae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-06-30 Released: 2017-07-12 
• Deposition Author(s): Jagielska, E., Nowak, E., Bochtler, M., Sabala, I.
• Funding Organization(s): The National Center for Research and Development

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.235 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Complex structure of lysostaphin SH3doamin with peptidoglycan fragment

Jagielska, E., Nowak, E., Bochtler, M., Sabala, I.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 22.56 kDa 
• Atom Count: 1,838 
• Modeled Residue Count: 196 
• Deposited Residue Count: 198 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysostaphin	A, B	94	Staphylococcaceae	Mutation(s): 0  Gene Names: lss EC: 3.4.24.75
UniProt
Find proteins for P10547 (Staphylococcus simulans) Explore P10547  Go to UniProtKB:  P10547

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GLY-GLY-GLY-GLY-GLY	C [auth G], D [auth H]	5	Staphylococcaceae	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	G [auth A], L [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO4	E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.235 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.38	α = 90
b = 54.364	β = 90
c = 63.229	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-07-12 
Deposition Author(s): Jagielska, E., Nowak, E., Bochtler, M., Sabala, I.

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Funding Organization	Location	Grant Number
The National Center for Research and Development	Poland	PBS1/A8/8/2012

Revision History  

• Version 1.0: 2017-07-12
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description