7V9Z | pdb_00007v9z

PaOrn Oligoribonuclease native structure

PDB DOI: https://doi.org/10.2210/pdb7V9Z/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

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: 1.85 Å
R-Value Free:
0.192 (Depositor), 0.193 (DCC)
R-Value Work:
0.164 (Depositor), 0.164 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

PaOrn Oligoribonuclease native structure

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

To be published.

Macromolecule Content

Total Structure Weight: 41.97 kDa
Atom Count: 3,247
Modeled Residue Count: 353
Deposited Residue Count: 360
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligoribonuclease	A, B	180	Pseudomonas aeruginosa PAO1	Mutation(s): 0 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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P57665
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
IMD (Subject of Investigation/LOI) Query on IMD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.192 (Depositor), 0.193 (DCC)
R-Value Work: 0.164 (Depositor), 0.164 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.68	α = 90
b = 82.68	β = 90
c = 193.047	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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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
Version 1.2: 2024-11-06
Changes: Structure summary

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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.