7OIW | pdb_00007oiw

Structure of S. aureus Rel catalytic domains in complex with pppGpp

PDB DOI: https://doi.org/10.2210/pdb7OIW/pdb

Classification: TRANSFERASE
Organism(s): Staphylococcus aureus subsp. aureus Mu50
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-05-12 Released: 2022-06-01
Deposition Author(s): Garcia-Pino, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.63 Å
R-Value Free:
0.261 (Depositor), 0.266 (DCC)
R-Value Work:
0.215 (Depositor), 0.223 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Structure of S. aureus Rel catalytic domains in complex with pppGpp

Garcia-Pino, A.

To be published.

Macromolecule Content

Total Structure Weight: 107.23 kDa
Atom Count: 5,484
Modeled Residue Count: 654
Deposited Residue Count: 876
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP pyrophosphokinase	A, B	438	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0 Gene Names: relA, SAV1634 EC: 2.7.6.5
UniProt
Find proteins for Q931Q4 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore Q931Q4 Go to UniProtKB: Q931Q4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q931Q4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0O2 (Subject of Investigation/LOI) Query on 0O2 Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], O [auth B], P [auth B]	guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate) C₁₀ H₁₈ N₅ O₂₀ P₅ KCPMACXZAITQAX-UUOKFMHZSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain O [auth B] Focus chain P [auth B]
VF5 Query on VF5 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]	[[(3~{a}~{R},4~{R},6~{R},6~{a}~{R})-4-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-2-oxidanyl-2-oxidanylidene-3~{a},4,6,6~{a}-tetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-6-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate C₁₀ H₁₅ N₅ O₁₆ P₄ RSYPFLCCTRWIKG-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain U [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain V [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain N [auth A] MOL2 format, chain U [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain V [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain N [auth A] mmCIF format, chain U [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain V [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	K [auth A] L [auth A] M [auth A] N [auth A] R [auth B] K [auth A], L [auth A], M [auth A], N [auth A], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-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 Q [auth B] SDF format, chain G [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain G [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain G [auth A]	G [auth A], Q [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain Q [auth B] Interactions & Density Focus chain G [auth A] Focus chain Q [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	H [auth A], I [auth A], J [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.63 Å
R-Value Free: 0.261 (Depositor), 0.266 (DCC)
R-Value Work: 0.215 (Depositor), 0.223 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.41	α = 90
b = 132.54	β = 103.59
c = 73.47	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2022-06-01

Deposition Author(s):

Garcia-Pino, A.

Revision History (Full details and data files)

Version 1.0: 2022-06-01
Type: Initial release
Version 2.0: 2023-09-27
Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-01-31
Changes: Refinement description