7VA3 | pdb_00007va3

PaOrn Oligoribonuclease D11A mutant with substrate pGpG complex structure

• PDB DOI: https://doi.org/10.2210/pdb7VA3/pdb
• NAKB: 7VA3

• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

PaOrn Oligoribonuclease D11A mutant with substrate pGpG complex structure

Zhang, J., Zhang, Q., Bartlam, M.

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)

Macromolecule Content 

• Total Structure Weight: 42.44 kDa 
• Atom Count: 3,225 
• Modeled Residue Count: 360 
• Deposited Residue Count: 362 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

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 (PDB Primary Data), 3.1.15 (UniProt)
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 ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*GP*G)-3')	C	2	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD (Subject of Investigation/LOI)	D [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
MN	E [auth A], F [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.223	α = 90
b = 83.223	β = 90
c = 192.553	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-09-07 
Deposition Author(s): Zhang, J., Zhang, Q., Bartlam, M.

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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  

• Version 1.0: 2022-09-07
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary