4Q7F

1.98 Angstrom Crystal Structure of Putative 5'-Nucleotidase from Staphylococcus aureus in complex with Adenosine.

• PDB DOI: https://doi.org/10.2210/pdb4Q7F/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Staphylococcus aureus subsp. aureus COL
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2014-04-24 Released: 2014-05-07 
• Deposition Author(s): Minasov, G., Nocadello, S., Shuvalova, L., Dubrovska, I., Winsor, J., Bagnoli, F., Falugi, F., Bottomley, M., Grandi, G., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.218 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 

Literature

1.98 Angstrom Crystal Structure of Putative 5'-Nucleotidase from Staphylococcus aureus in complex with Adenosine.

Minasov, G., Nocadello, S., Shuvalova, L., Dubrovska, I., Winsor, J., Bagnoli, F., Falugi, F., Bottomley, M., Grandi, G., 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: 60.97 kDa 
• Atom Count: 4,629 
• Modelled Residue Count: 510 
• Deposited Residue Count: 527 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5' nucleotidase family protein	A	527	Staphylococcus aureus subsp. aureus COL	Mutation(s): 0  Gene Names: SACOL0130, SAOUHSC_00107
UniProt
Find proteins for Q2G1L5 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G1L5  Go to UniProtKB:  Q2G1L5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3D1	D [auth A]	(2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol C10 H13 N5 O3 OLXZPDWKRNYJJZ-RRKCRQDMSA-N
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.218 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 
• Space Group: C 1 2 1
• Diffraction Data: https://doi.org/10.18430/M34Q7F

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.584	α = 90
b = 86.452	β = 116.86
c = 95.647	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-07 
Deposition Author(s): Minasov, G., Nocadello, S., Shuvalova, L., Dubrovska, I., Winsor, J., Bagnoli, F., Falugi, F., Bottomley, M., Grandi, G., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2014-05-07
  Type: Initial release
  
• Version 1.1: 2014-05-21
  Changes: Other
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-12-06
  Changes: Data collection