8RIX | pdb_00008rix

Crystal structure of chloroplast FtsY from Arabidopsis thaliana in complex with the alarmone ppGpp

PDB DOI: https://doi.org/10.2210/pdb8RIX/pdb

Classification: PROTEIN TRANSPORT
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-12-19 Released: 2025-01-01
Deposition Author(s): Czech, L., Bange, G.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free:
0.276 (Depositor), 0.274 (DCC)
R-Value Work:
0.219 (Depositor), 0.218 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure of chloroplast FtsY from Arabidopsis thaliana in complex with the alarmone ppGpp

Czech, L., Bange, G.

To be published.

Macromolecule Content

Total Structure Weight: 34.68 kDa
Atom Count: 2,363
Modeled Residue Count: 295
Deposited Residue Count: 314
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division protein FtsY homolog, chloroplastic	A	314	Arabidopsis thaliana	Mutation(s): 0 Gene Names: CPFTSY, FTSY, At2g45770, F4I18.25
UniProt
Find proteins for O80842 (Arabidopsis thaliana) Explore O80842 Go to UniProtKB: O80842
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O80842
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G4P (Subject of Investigation/LOI) Query on G4P 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]	GUANOSINE-5',3'-TETRAPHOSPHATE C₁₀ H₁₇ N₅ O₁₇ P₄ BUFLLCUFNHESEH-UUOKFMHZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG (Subject of Investigation/LOI) Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.276 (Depositor), 0.274 (DCC)
R-Value Work: 0.219 (Depositor), 0.218 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.28	α = 90
b = 37.07	β = 110.628
c = 59.82	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-01-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-01-01
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.