8ED5 | pdb_00008ed5

Crystal structure of loop deletion AioX mutant from Pseudorhizobium sp. str. NT-26

PDB DOI: https://doi.org/10.2210/pdb8ED5/pdb

Classification: SIGNALING PROTEIN
Organism(s): Pseudorhizobium banfieldiae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-09-03 Released: 2023-11-08
Deposition Author(s): Maher, M.J., Poddar, N.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.198 (Depositor), 0.210 (DCC)
R-Value Work:
0.185 (Depositor), 0.200 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Investigating the interaction of the periplasmic arsenite-binding protein, AioX with the sensor histidine kinase, AioS from Pseudorhizobium banfieldii sp. str. NT-26

Maher, M.J., Poddar, N.

To be published.

Macromolecule Content

Total Structure Weight: 33.37 kDa
Atom Count: 2,313
Modeled Residue Count: 261
Deposited Residue Count: 299
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative periplasmic phosphite-binding-like protein (Pbl) PtxB-like protein designated AioX	A	299	Pseudorhizobium banfieldiae	Mutation(s): 1 Gene Names: aioX, NT26_p10026
UniProt
Find proteins for L0NML6 (Pseudorhizobium banfieldiae) Explore L0NML6 Go to UniProtKB: L0NML6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	L0NML6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.198 (Depositor), 0.210 (DCC)
R-Value Work: 0.185 (Depositor), 0.200 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.155	α = 90
b = 125.155	β = 90
c = 47.415	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-11-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-11-08
Type: Initial release

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.