5FT9 | pdb_00005ft9

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.05 Å
R-Value Free:
0.290 (Depositor), 0.300 (DCC)
R-Value Work:
0.242 (Depositor), 0.254 (DCC)
R-Value Observed:
0.244 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q680B9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.05 Å
R-Value Free: 0.290 (Depositor), 0.300 (DCC)
R-Value Work: 0.242 (Depositor), 0.254 (DCC)
R-Value Observed: 0.244 (Depositor)

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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-01-27

Deposition Author(s):

Fernandez-Millan, P.

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.