6BV8 | pdb_00006bv8

Structure of proteinaceous RNase P 1 (PRORP1) from A. thaliana complexed with Mn after 3-hour soak with juglone

• PDB DOI: https://doi.org/10.2210/pdb6BV8/pdb

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


• Deposited: 2017-12-12 Released: 2019-06-12 
• Deposition Author(s): Karasik, A., Wu, N., Fierke, C.A., Koutmos, M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.236 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Inhibition of protein-only RNase P with Gambogic acid and Juglone

Wu, N., Karasik, A., Muehlbauer, L., Koutmos, M., Fierke, C.A.

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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 57.03 kDa 
• Atom Count: 4,028 
• Modeled Residue Count: 472 
• Deposited Residue Count: 501 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteinaceous RNase P 1, chloroplastic/mitochondrial	A	501	Arabidopsis thaliana	Mutation(s): 0  Gene Names: PRORP1, At2g32230, F22D22.2 EC: 3.1.26.5
UniProt
Find proteins for Q66GI4 (Arabidopsis thaliana) Explore Q66GI4  Go to UniProtKB:  Q66GI4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JUG	B [auth A]	5-hydroxynaphthalene-1,4-dione C10 H6 O3 KQPYUDDGWXQXHS-UHFFFAOYSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.236 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.677	α = 90
b = 111.332	β = 90
c = 139.389	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-06-12 
Deposition Author(s): Karasik, A., Wu, N., Fierke, C.A., Koutmos, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM117141

Revision History  

• Version 1.0: 2019-06-12
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary