3KZP

Crystal structure of putative diguanylate cyclase/phosphodiesterase from Listaria monocytigenes

• PDB DOI: https://doi.org/10.2210/pdb3KZP/pdb

• Classification: Structural Genomics, Unknown function
• Organism(s): Listeria monocytogenes
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-12-08 Released: 2009-12-22 
• Deposition Author(s): Klimecka, M.M., Chruszcz, M., Zimmerman, M.D., Kudritska, M., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.239 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Crystal structure of putative diguanylate cyclase/phosphodiesterase from Listaria monocytigenes

Klimecka, M.M., Chruszcz, M., Zimmerman, M.D., Kudritska, M., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W.

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: 55.56 kDa 
• Atom Count: 4,243 
• Modelled Residue Count: 463 
• Deposited Residue Count: 470 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative diguanylate cyclase/phosphodiesterase	A, B	235	Listeria monocytogenes	Mutation(s): 0  Gene Names: lmo0111
UniProt
Find proteins for Q8YAK7 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8YAK7  Go to UniProtKB:  Q8YAK7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAC	H [auth A], L [auth B]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
CA	G [auth A], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	C [auth A], D [auth A], E [auth A], F [auth A], I [auth B], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 2.00 Å
• R-Value Free:  0.239 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.766	α = 90
b = 92.04	β = 90
c = 96.21	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
ARP/wARP	model building
REFMAC	refinement
Coot	model building
HKL-3000	data reduction
HKL-2000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-22 
Deposition Author(s): Klimecka, M.M., Chruszcz, M., Zimmerman, M.D., Kudritska, M., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-12-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-11-20
  Changes: Data collection, Structure summary