9DQW

Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli in complex with UMA and AMP-PNP

• PDB DOI: https://doi.org/10.2210/pdb9DQW/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-09-24 Released: 2024-10-09 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.165 
• R-Value Work: 0.150 
• R-Value Observed: 0.150 

Starting Model: experimental

Literature

Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli in complex with UMA and AMP-PNP

Seibold, S., Liu, L., Lovell, S., Battaile, K.P.

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

Macromolecule Content

• Total Structure Weight: 49.95 kDa 
• Atom Count: 3,884 
• Modelled Residue Count: 439 
• Deposited Residue Count: 445 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylmuramoylalanine--D-glutamate ligase	A	445	Escherichia coli K-12	Mutation(s): 0  Gene Names: murD, b0088, JW0086 EC: 6.3.2.9
UniProt
Find proteins for P14900 (Escherichia coli (strain K12)) Explore P14900  Go to UniProtKB:  P14900

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UMA (Subject of Investigation/LOI)	C [auth A]	URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE C23 H36 N4 O20 P2 NTMMCWJNQNKACG-KBKUWGQMSA-N
ANP (Subject of Investigation/LOI)	G [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
EPE	H [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
SO4	K [auth A], L [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	I [auth A], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.165 
• R-Value Work: 0.150 
• R-Value Observed: 0.150 
• Space Group: P 4₁
• Diffraction Data: https://doi.org/10.18430/M39DQW

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.441	α = 90
b = 65.441	β = 90
c = 135.609	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): 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	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release