3QFK

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
R-Value Work: 0.173
R-Value Observed: 0.176

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 61.1 kDa
Atom Count: 4,477
Modelled Residue Count: 510
Deposited Residue Count: 527
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2G1L5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AKG Query on AKG Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	2-OXOGLUTARIC ACID C₅ H₆ O₅ KPGXRSRHYNQIFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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
R-Value Work: 0.173
R-Value Observed: 0.176
Space Group: C 1 2 1
Diffraction Data: https://doi.org/10.18430/m33qfk

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

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Entry History

Deposition Data

Released Date: 2011-02-09

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

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

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3QFK

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)