7Q8E | pdb_00007q8e

Crystal Structure of the MurT-GatD Enzyme Complex from Staphylococcus aureus COL strain

• PDB DOI: https://doi.org/10.2210/pdb7Q8E/pdb

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


• Deposited: 2021-11-11 Released: 2023-05-24 
• Deposition Author(s): Leisico, F., Romao, M.J., Santos-Silva, T.
• Funding Organization(s): Fundacao para a Ciencia e a Tecnologia

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the MurT-GatD Enzyme Complex from Staphylococcus aureus COL strain

Leisico, F., Romao, M.J., Santos-Silva, T.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 155.77 kDa 
• Atom Count: 10,134 
• Modeled Residue Count: 1,280 
• Deposited Residue Count: 1,376 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT	A, B [auth C]	437	Staphylococcus aureus subsp. aureus COL	Mutation(s): 0  Gene Names: murT, SACOL1951 EC: 6.3.5.13
UniProt
Find proteins for A0A0H2WZQ7 (Staphylococcus aureus (strain COL)) Explore A0A0H2WZQ7  Go to UniProtKB:  A0A0H2WZQ7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD	C [auth B], D	251	Staphylococcus aureus subsp. aureus COL	Mutation(s): 0  Gene Names: gatD, SACOL1950 EC: 6.3.5.13 (PDB Primary Data), 3.5.1.2 (PDB Primary Data)
UniProt
Find proteins for A0A0H2WZ38 (Staphylococcus aureus (strain COL)) Explore A0A0H2WZ38  Go to UniProtKB:  A0A0H2WZ38

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	E [auth A], G [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.094	α = 90
b = 111.094	β = 90
c = 112.424	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-24 
Deposition Author(s): Leisico, F., Romao, M.J., Santos-Silva, T.

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Funding Organization	Location	Grant Number
Fundacao para a Ciencia e a Tecnologia	Portugal	PD/BD/105737/2014
Fundacao para a Ciencia e a Tecnologia	Portugal	UIDP/04378/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	UIDB/04378/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	LA/P/0140/2020

Revision History  

• Version 1.0: 2023-05-24
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description