7SY9

Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from Pseudomonas aeruginosa PAO1

• PDB DOI: https://doi.org/10.2210/pdb7SY9/pdb

• Classification: LIGASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-11-24 Released: 2021-12-15 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.247 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 

Starting Model: experimental

Literature

Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from Pseudomonas aeruginosa PAO1

Abendroth, J., Davies, D.R., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 96.78 kDa 
• Atom Count: 6,236 
• Modelled Residue Count: 858 
• Deposited Residue Count: 896 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylmuramoylalanine--D-glutamate ligase	A, B	448	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: murD, PA4414 EC: 6.3.2.9
UniProt
Find proteins for Q9HVZ9 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HVZ9  Go to UniProtKB:  Q9HVZ9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT	D [auth A], E [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.247 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 
• Space Group: P 6₅ 2 2
• Diffraction Data: https://doi.org/10.18430/M37SY9

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.75	α = 90
b = 94.75	β = 90
c = 442.92	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
Coot	model building
PHENIX	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-12-15 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700059C

Revision History  

• Version 1.0: 2021-12-15
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description