2PXB

Variant 2 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle

• PDB DOI:  https://doi.org/10.2210/pdb2PXB/pdb
• NAKB: 2PXB

• Classification: SIGNALING PROTEIN/RNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-05-14 Released: 2007-08-07 
• Deposition Author(s): Keel, A.Y., Rambo, R.P., Batey, R.T., Kieft, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.272 
• R-Value Work: 0.254 

Literature

A General Strategy to Solve the Phase Problem in RNA Crystallography.

Keel, A.Y., Rambo, R.P., Batey, R.T., Kieft, J.S.

(2007) Structure 15: 761-772

• PubMed: 17637337 
• DOI: https://doi.org/10.1016/j.str.2007.06.003
• Primary Citation of Related Structures:  
  2PXB, 2PXD, 2PXE, 2PXF, 2PXK, 2PXL, 2PXP, 2PXQ, 2PXT, 2PXU, 2PXV


• PubMed Abstract: 
  

X-ray crystallography of biologically important RNA molecules has been hampered by technical challenges, including finding heavy-atom derivatives to obtain high-quality experimental phase information. Existing techniques have drawbacks, limiting the rate at which important new structures are solved. To address this, we have developed a reliable means to localize heavy atoms specifically to virtually any RNA. By solving the crystal structures of thirteen variants of the G*U wobble pair cation binding motif, we have identified a version that when inserted into an RNA helix introduces a high-occupancy cation binding site suitable for phasing. This "directed soaking" strategy can be integrated fully into existing RNA crystallography methods, potentially increasing the rate at which important structures are solved and facilitating routine solving of structures using Cu-Kalpha radiation. This method already has been used to solve several crystal structures.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Genetics, University of Colorado at Denver and Health Sciences Center, Aurora, CO 80045, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.51 kDa 
• Atom Count: 1,641 
• Modelled Residue Count: 118 
• Deposited Residue Count: 151 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Signal recognition particle protein	B [auth A]	102	Escherichia coli	Mutation(s): 14  Gene Names: ffh
UniProt
Find proteins for P0AGD7 (Escherichia coli (strain K12)) Explore P0AGD7  Go to UniProtKB:  P0AGD7

Entity ID: 1
Molecule	Chains	Length	Organism	Image
4.5 S RNA	A [auth B]	49	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCO	C [auth B], D [auth B], E [auth B], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-FGTKAUEHAT

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	B [auth A]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.272 
• R-Value Work: 0.254 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.981	α = 90
b = 78.684	β = 94.86
c = 32.274	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-07 
Deposition Author(s): Keel, A.Y., Rambo, R.P., Batey, R.T., Kieft, J.S.

Revision History  

• Version 1.0: 2007-08-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-05-10
  Changes: Refinement description
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations, Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Refinement description