8QJM

SmNuc1 nuclease from Stenotrophomonas maltophilia in complex with cytidine-5'-monophosphate

• PDB DOI: https://doi.org/10.2210/pdb8QJM/pdb

• Classification: HYDROLASE
• Organism(s): Stenotrophomonas maltophilia
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-09-13 Released: 2024-09-25 
• Deposition Author(s): Adamkova, K., Koval, T., Kolenko, P., Dohnalek, J.
• Funding Organization(s): Czech Science Foundation, Czech Academy of Sciences, Ministry of Education, Youth and Sports of the Czech Republic, European Regional Development Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.198 
• R-Value Work: 0.173 
• R-Value Observed: 0.173 

Starting Model: experimental

Literature

Substrate preference, RNA binding and active site versatility of the Stenotrophomonas maltophilia nuclease SmNuc1, explained by a structural study

Adamkova, K., Trundova, M., Koval, T., Hustakova, B., Duskova, J., Skalova, T., Kolenko, P., Dohnalek, J.

(2024) The Febs Journal 

• DOI: https://doi.org/10.1111/febs.17265

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 59.58 kDa 
• Atom Count: 4,659 
• Modelled Residue Count: 497 
• Deposited Residue Count: 508 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S1/P1 Nuclease	A, B	254	Stenotrophomonas maltophilia	Mutation(s): 0  Gene Names: A1OC_03585

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C5P (Subject of Investigation/LOI)	C [auth A], P [auth B], Q [auth B]	CYTIDINE-5'-MONOPHOSPHATE C9 H14 N3 O8 P IERHLVCPSMICTF-XVFCMESISA-N
1PE	U [auth B]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
SO4	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth A], R [auth B], S [auth B], T [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	O [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.198 
• R-Value Work: 0.173 
• R-Value Observed: 0.173 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.139	α = 90
b = 72.805	β = 105.066
c = 81.238	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-25 
Deposition Author(s): Adamkova, K., Koval, T., Kolenko, P., Dohnalek, J.

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Funding Organization	Location	Grant Number
Czech Science Foundation	Czech Republic	23-06295S
Czech Academy of Sciences	Czech Republic	86652036
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	LM2023042
European Regional Development Fund	European Union	CZ.02.1.01/0.0/0.0/18_046/0015974

Revision History  

• Version 1.0: 2024-09-25
  Type: Initial release