3EAG

The crystal structure of UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase (MPL) from Neisseria meningitides

• PDB DOI: https://doi.org/10.2210/pdb3EAG/pdb

• Classification: LIGASE
• Organism(s): Neisseria meningitidis MC58
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-25 Released: 2008-09-09 
• Deposition Author(s): Chang, C., Hendricks, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.243 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 

Literature

The crystal structure of UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase (MPL) from Neisseria meningitides

Chang, C., Hendricks, R., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 71.96 kDa 
• Atom Count: 5,061 
• Modelled Residue Count: 648 
• Deposited Residue Count: 652 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase	A, B	326	Neisseria meningitidis MC58	Mutation(s): 0  Gene Names: mpl-2, mpl-1, NMB1145, NMB1183 EC: 6.3.2 (PDB Primary Data), 6.3.2.45 (UniProt)
UniProt
Find proteins for Q9JRY9 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58)) Explore Q9JRY9  Go to UniProtKB:  Q9JRY9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.243 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.497	α = 90
b = 83.8	β = 90
c = 143.838	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-09 
Deposition Author(s): Chang, C., Hendricks, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-09-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary