8R9R | pdb_00008r9r

GDP-bound state of S. putrefaciens FlhF

• PDB DOI: https://doi.org/10.2210/pdb8R9R/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Shewanella putrefaciens CN-32
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-11-30 Released: 2024-03-20 
• Deposition Author(s): Mais, C.N., Dornes, A., Bange, G.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 
  0.250 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Structure of the GDP-bound state of the SRP GTPase FlhF.

Dornes, A., Mais, C.N., Bange, G.

(2024) Acta Crystallogr F Struct Biol Commun 80: 53-58

• PubMed: 38376823 
• DOI: https://doi.org/10.1107/S2053230X24000979
• Primary Citation of Related Structures:  
  8R9R


• PubMed Abstract: 
  

  The GTPase FlhF, a signal recognition particle (SRP)-type enzyme, is pivotal for spatial-numerical control and bacterial flagella assembly across diverse species, including pathogens. This study presents the X-ray structure of FlhF in its GDP-bound state at a resolution of 2.28 Å. The structure exhibits the classical N- and G-domain fold, consistent with related SRP GTPases such as Ffh and FtsY. Comparative analysis with GTP-loaded FlhF elucidates the conformational changes associated with GTP hydrolysis. These topological reconfigurations are similarly evident in Ffh and FtsY, and play a pivotal role in regulating the functions of these hydrolases.

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Organizational Affiliation: 

Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, University of Marburg, Karl-von-Frisch-Strasse 14, 35043 Marburg, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 32.73 kDa 
• Atom Count: 1,965 
• Modelled Residue Count: 255 
• Deposited Residue Count: 295 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar biosynthesis protein FlhF	A	295	Shewanella putrefaciens CN-32	Mutation(s): 0  Gene Names: Sputcn32_2561
UniProt
Find proteins for A4Y8J9 (Shewanella putrefaciens (strain CN-32 / ATCC BAA-453)) Explore A4Y8J9  Go to UniProtKB:  A4Y8J9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP (Subject of Investigation/LOI)	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free:  0.250 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.92	α = 90
b = 73.92	β = 90
c = 159.96	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-20 
Deposition Author(s): Mais, C.N., Dornes, A., Bange, G.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	495924434

Revision History  

• Version 1.0: 2024-03-20
  Type: Initial release