3TAU | pdb_00003tau

Crystal Structure of a Putative Guanylate Monophosphaste Kinase from Listeria monocytogenes EGD-e

• PDB DOI: https://doi.org/10.2210/pdb3TAU/pdb

• Classification: TRANSFERASE
• Organism(s): Listeria monocytogenes
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-08-04 Released: 2011-08-24 
• Deposition Author(s): Brunzelle, J.S., Wawrzak, Z., Onopriyenko, O., Kwok, J., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.220 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Crystal Structure of a Putative Guanylate Monophosphaste Kinase from Listeria monocytogenes EGD-e

Brunzelle, J.S., Wawrzak, Z., Onopriyenko, O., Kwok, J., Anderson, W.F., Savchenko, 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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.41 kDa 
• Atom Count: 3,367 
• Modeled Residue Count: 376 
• Deposited Residue Count: 416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanylate kinase	A, B	208	Listeria monocytogenes	Mutation(s): 0  Gene Names: gmk, lmo1827 EC: 2.7.4.8
UniProt
Find proteins for Q8Y672 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y672  Go to UniProtKB:  Q8Y672

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-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: 2.05 Å
• R-Value Free:  0.220 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33tau

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.733	α = 90
b = 65.321	β = 90
c = 107.32	γ = 90

Software Package:

Software Name	Purpose
BLU-MAX	data collection
PHENIX	model building
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-24 
Deposition Author(s): Brunzelle, J.S., Wawrzak, Z., Onopriyenko, O., Kwok, J., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-08-24
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary