7VA6

PaOrn Oligoribonuclease D11A mutant with RNA GU complex structure

PDB DOI: https://doi.org/10.2210/pdb7VA6/pdb
NAKB: 7VA6

Classification: HYDROLASE
Organism(s): Pseudomonas aeruginosa PAO1, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-08-27 Released: 2022-09-07
Deposition Author(s): Zhang, J., Zhang, Q., Bartlam, M.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.196
R-Value Work: 0.167
R-Value Observed: 0.168

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

PaOrn Oligoribonuclease D11A mutant with RNA GU complex structure

Zhang, J., Zhang, Q., Bartlam, M.

To be published.

Macromolecule Content

Total Structure Weight: 42.29 kDa
Atom Count: 3,137
Modelled Residue Count: 354
Deposited Residue Count: 362
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligoribonuclease	A, B	180	Pseudomonas aeruginosa PAO1	Mutation(s): 1 Gene Names: orn, PA4951 EC: 3.1
UniProt
Find proteins for P57665 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P57665 Go to UniProtKB: P57665
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P57665
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(PGPU)-3')	C	2	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IMD (Subject of Investigation/LOI) Query on IMD Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.196
R-Value Work: 0.167
R-Value Observed: 0.168
Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.993	α = 90
b = 82.993	β = 90
c = 192.923	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-09-07

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31870053
National Natural Science Foundation of China (NSFC)	China	31800627

Revision History (Full details and data files)

Version 1.0: 2022-09-07
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.