6VUD | pdb_00006vud

Crystal structure of a ribosome recycling factor from Ehrlichia chaffeensis

• PDB DOI: https://doi.org/10.2210/pdb6VUD/pdb

• Classification: TRANSLATION
• Organism(s): Ehrlichia chaffeensis str. Arkansas
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2020-02-15 Released: 2020-03-18 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Models: experimental

Literature

Crystal structure of a ribosome recycling factor from Ehrlichia chaffeensis

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Abendroth, J., Horanyi, P.S., Lorimer, D.D., Edwards, T.E.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 43.66 kDa 
• Atom Count: 2,820 
• Modeled Residue Count: 370 
• Deposited Residue Count: 386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome-recycling factor	A, B	193	Ehrlichia chaffeensis str. Arkansas	Mutation(s): 0  Gene Names: frr, ECH_0267
UniProt
Find proteins for Q2GHJ5 (Ehrlichia chaffeensis (strain ATCC CRL-10679 / Arkansas)) Explore Q2GHJ5  Go to UniProtKB:  Q2GHJ5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth A], E [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36vud

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.66	α = 90
b = 93.23	β = 109.728
c = 73.42	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MR-Rosetta	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-03-18 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2020-03-18
  Type: Initial release
  
• Version 1.1: 2020-07-01
  Changes: Data collection
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references
• Version 1.3: 2024-04-03
  Changes: Refinement description