3GKR | pdb_00003gkr

Crystal Structure of Weissella viridescens FemX:UDP-MurNAc-hexapeptide complex

• PDB DOI: https://doi.org/10.2210/pdb3GKR/pdb

• Classification: Transferase/Transferase Product
• Organism(s): Weissella viridescens, Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-11 Released: 2010-03-23 
• Deposition Author(s): Delfosse, V., Piton, J., Villet, R., Lecerf, M., Arthur, M., Mayer, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.216 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Structure of Weissella viridescens FemX with the UDP-MurNAc-hexapeptide product of the alanine transfer reaction

Delfosse, V., Piton, J., Villet, R., Lecerf, M., Arthur, M., Mayer, C.

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)

Macromolecule Content 

• Total Structure Weight: 39.73 kDa 
• Atom Count: 3,292 
• Modeled Residue Count: 340 
• Deposited Residue Count: 341 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FemX	A	336	Weissella viridescens	Mutation(s): 0  Gene Names: femX EC: 2.3.2.10
UniProt
Find proteins for Q9EY50 (Weissella viridescens) Explore Q9EY50  Go to UniProtKB:  Q9EY50

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-MurNAc-peptide	B	5	Staphylococcus aureus	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ALA	G [auth B]	ALANINE C3 H7 N O2 QNAYBMKLOCPYGJ-REOHCLBHSA-N
MG	C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DAL	B	D-PEPTIDE LINKING	C3 H7 N O2		--
UMA	B	L-PEPTIDE LINKING	C23 H36 N4 O20 P2		ALA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.216 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.324	α = 90
b = 101.836	β = 102.85
c = 46.847	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-23 
Deposition Author(s): Delfosse, V., Piton, J., Villet, R., Lecerf, M., Arthur, M., Mayer, C.

Revision History  

• Version 1.0: 2010-03-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Database references, Derived calculations, Non-polymer description, Version format compliance
• Version 1.2: 2012-08-01
  Changes: Structure summary
• Version 1.3: 2012-09-05
  Changes: Derived calculations
• Version 1.4: 2023-11-01
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description