2NG1 | pdb_00002ng1

N AND GTPASE DOMAINS OF THE SIGNAL SEQUENCE RECOGNITION PROTEIN FFH FROM THERMUS AQUATICUS

• PDB DOI: https://doi.org/10.2210/pdb2NG1/pdb

• Classification: SIGNAL RECOGNITION
• Organism(s): Thermus aquaticus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1998-09-11 Released: 1999-07-30 
• Deposition Author(s): Freymann, D.M., Stroud, R.M., Walter, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.290 (Depositor) 
• R-Value Work: 
  0.200 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Functional changes in the structure of the SRP GTPase on binding GDP and Mg2+GDP.

Freymann, D.M., Keenan, R.J., Stroud, R.M., Walter, P.

(1999) Nat Struct Biol 6: 793-801

• PubMed: 10426959 
• DOI: https://doi.org/10.1038/11572
• Primary Citation Related Structures: 
  1NG1, 2NG1, 3NG1


• PubMed Abstract: 
  

  Ffh is a component of a bacterial ribonucleoprotein complex homologous to the signal recognition particle (SRP) of eukaryotes. It comprises three domains that mediate both binding to the hydrophobic signal sequence of the nascent polypeptide and the GTP-dependent interaction of Ffh with a structurally homologous GTPase of the SRP receptor. The X-ray structures of the two-domain 'NG' GTPase of Ffh in complex with Mg2+GDP and GDP have been determined at 2.0 A resolution. The structures explain the low nucleotide affinity of Ffh and locate two regions of structural mobility at opposite sides of the nucleotide-binding site. One of these regions includes highly conserved sequence motifs that presumably contribute to the structural trigger signaling the GTP-bound state. The other includes the highly conserved interface between the N and G domains, and supports the hypothesis that the N domain regulates or signals the nucleotide occupancy of the G domain.

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Organizational Affiliation: 
• Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Medical School, 303 E. Chicago Avenue, Chicago, Illinois 60611, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 32.85 kDa 
• Atom Count: 2,375 
• Modeled Residue Count: 293 
• Deposited Residue Count: 293 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SIGNAL SEQUENCE RECOGNITION PROTEIN FFH	A	293	Thermus aquaticus	Mutation(s): 1  Gene Names: FFH EC: 3.6.5.4
UniProt
Find proteins for O07347 (Thermus aquaticus) Explore O07347  Go to UniProtKB:  O07347

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
DIO	C [auth A]	1,4-DIETHYLENE DIOXIDE C4 H8 O2 RYHBNJHYFVUHQT-UHFFFAOYSA-N
EDO	D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.290 (Depositor) 
• R-Value Work:  0.200 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.425	α = 90
b = 54.214	β = 119.62
c = 58.465	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-07-30 
Deposition Author(s): Freymann, D.M., Stroud, R.M., Walter, P.

Revision History  

• Version 1.0: 1999-07-30
  Type: Initial release
  
• Version 1.1: 2008-03-05
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-03-14
  Changes: Database references
• Version 1.4: 2023-08-09
  Changes: Database references, Derived calculations, Refinement description
• Version 1.5: 2024-05-22
  Changes: Data collection