3QFK | pdb_00003qfk

2.05 Angstrom Crystal Structure of Putative 5'-Nucleotidase from Staphylococcus aureus in complex with alpha-ketoglutarate

• PDB DOI: https://doi.org/10.2210/pdb3QFK/pdb

• Classification: HYDROLASE
• Organism(s): Staphylococcus aureus subsp. aureus NCTC 8325
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-01-21 Released: 2011-02-09 
• Deposition Author(s): Minasov, G., Wawrzak, Z., Krishna, S.N., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Kiryukhina, O., Bagnoli, F., Falugi, F., Bottomley, M., Grandi, G., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.221 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

2.05 Angstrom Crystal Structure of Putative 5'-Nucleotidase from Staphylococcus aureus in complex with alpha-ketoglutarate.

Minasov, G., Wawrzak, Z., Krishna, S.N., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Kiryukhina, O., 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: 61.1 kDa 
• Atom Count: 4,477 
• Modeled Residue Count: 510 
• Deposited Residue Count: 527 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKG	D [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-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: 2.05 Å
• R-Value Free:  0.221 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33qfk

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.444	α = 90
b = 84.689	β = 116.91
c = 95.966	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-09 
Deposition Author(s): Minasov, G., Wawrzak, Z., Krishna, S.N., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Kiryukhina, O., Bagnoli, F., Falugi, F., Bottomley, M., Grandi, G., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-02-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary