7BB9 | pdb_00007bb9

Crystal structure of Lugdulysin E242Q Y315F mutant

• PDB DOI: https://doi.org/10.2210/pdb7BB9/pdb

• Classification: HYDROLASE
• Organism(s): Staphylococcus lugdunensis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-12-17 Released: 2022-07-13 
• Deposition Author(s): Ruff, M., Prevost, G., Prola, K., Levy, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 

Starting Model: experimental

Literature

Crystal structure of Lugdulysin E242Q Y315F mutant

Ruff, M., Prevost, G., Prola, K., Levy, N.

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: 47.38 kDa 
• Atom Count: 3,547 
• Modeled Residue Count: 399 
• Deposited Residue Count: 410 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lugdulysin E242Q Y315F	A	410	Staphylococcus lugdunensis	Mutation(s): 2  Gene Names: EQ812_06155
UniProt
Find proteins for A0A292DHH8 (Staphylococcus lugdunensis) Explore A0A292DHH8  Go to UniProtKB:  A0A292DHH8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	B [auth A], C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.25	α = 90
b = 96.25	β = 90
c = 84.17	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-07-13 
Deposition Author(s): Ruff, M., Prevost, G., Prola, K., Levy, N.

Revision History  

• Version 1.0: 2022-07-13
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description