3TX1

X-ray crystal structure of Listeria monocytogenes EGD-e UDP-N-acetylenolpyruvylglucosamine reductase (MurB)

• PDB DOI: https://doi.org/10.2210/pdb3TX1/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Listeria monocytogenes
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-09-22 Released: 2011-10-05 
• Deposition Author(s): Filippova, E.V., Minasov, G., Shuvalova, L., Dubrovska, I., Winsor, J., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 0.269 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 

Starting Model: experimental

Literature

X-ray crystal structure of Listeria monocytogenes EGD-e UDP-N-acetylenolpyruvylglucosamine reductase (MurB).

Filippova, E.V., Minasov, G., Shuvalova, L., Dubrovska, I., Winsor, J., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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: 36.15 kDa 
• Atom Count: 2,379 
• Modelled Residue Count: 295 
• Deposited Residue Count: 322 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylenolpyruvoylglucosamine reductase	A	322	Listeria monocytogenes	Mutation(s): 0  Gene Names: lmo1420, murB EC: 1.1.1.158 (PDB Primary Data), 1.3.1.98 (UniProt)
UniProt
Find proteins for Q8Y776 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y776  Go to UniProtKB:  Q8Y776

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
SO4	E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 0.269 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 
• Space Group: P 6₁ 2 2
• Diffraction Data: https://doi.org/10.18430/m33tx1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.21	α = 90
b = 95.21	β = 90
c = 189.895	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-05 
Deposition Author(s): Filippova, E.V., Minasov, G., Shuvalova, L., Dubrovska, I., Winsor, J., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-10-05
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description