5FT9

Arabidopsis thaliana nuclear protein-only RNase P 2 (PRORP2)

• PDB DOI: https://doi.org/10.2210/pdb5FT9/pdb

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


• Deposited: 2016-01-12 Released: 2016-01-27 
• Deposition Author(s): Fernandez-Millan, P., Pinker, F., Schelcher, C., Gobert, A., Giege, P., Sauter, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 0.290 
• R-Value Work: 0.242 
• R-Value Observed: 0.244 

Literature

Structures of Arabidopsis Nuclear Rnase P Alone and with tRNA Reveal Plasticities

Pinker, F., Schelcher, C., Fernandez-Millan, P., Gobert, A., Birck, C., Roblin, P., Giege, P., Sauter, C.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 120.99 kDa 
• Atom Count: 7,444 
• Modelled Residue Count: 945 
• Deposited Residue Count: 1,074 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEINACEOUS RNASE P 2	A, B	537	Arabidopsis thaliana	Mutation(s): 0  EC: 3.1.26.5
UniProt
Find proteins for Q680B9 (Arabidopsis thaliana) Explore Q680B9  Go to UniProtKB:  Q680B9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 0.290 
• R-Value Work: 0.242 
• R-Value Observed: 0.244 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.5	α = 63.1
b = 72.8	β = 72.2
c = 80.3	γ = 78.4

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-27 
Deposition Author(s): Fernandez-Millan, P., Pinker, F., Schelcher, C., Gobert, A., Giege, P., Sauter, C.

Revision History  

• Version 1.0: 2016-01-27
  Type: Initial release
  
• Version 1.1: 2019-03-06
  Changes: Data collection, Experimental preparation, Other
• Version 1.2: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description