4Q7F | pdb_00004q7f

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free:
0.218 (Depositor), 0.226 (DCC)
R-Value Work:
0.187 (Depositor), 0.198 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 60.97 kDa
Atom Count: 4,629
Modeled Residue Count: 510
Deposited Residue Count: 527
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2G1L5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3D1 Query on 3D1 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]	(2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol C₁₀ H₁₃ N₅ O₃ OLXZPDWKRNYJJZ-RRKCRQDMSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [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]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [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: 1.98 Å
R-Value Free: 0.218 (Depositor), 0.226 (DCC)
R-Value Work: 0.187 (Depositor), 0.198 (DCC)
R-Value Observed: 0.188 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-05-07

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

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
Version 1.5: 2024-10-30
Changes: Structure summary