9NXM | pdb_00009nxm

Crystal structure of Arabidopsis thaliana NUDT11 E90Q/E94Q mutant

PDB DOI: https://doi.org/10.2210/pdb9NXM/pdb

Classification: PLANT PROTEIN
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-03-25 Released: 2026-04-01
Deposition Author(s): Chu, H.F., Liang, T.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free:
0.249 (Depositor), 0.247 (DCC)
R-Value Work:
0.211 (Depositor), 0.211 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9NXM

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

Literature

Arabidopsis thaliana NUDT11 E90/94Q mutant

Chu, H.F., Liang, T.

To be published.

Macromolecule Content

Total Structure Weight: 25.98 kDa
Atom Count: 1,745
Modeled Residue Count: 213
Deposited Residue Count: 224
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nudix hydrolase 11	A	224	Arabidopsis thaliana	Mutation(s): 2 Gene Names: NUDT11, NUDX11, At5g45940, K15I22.14 EC: 3.6.1
UniProt
Find proteins for Q8LET2 (Arabidopsis thaliana) Explore Q8LET2 Go to UniProtKB: Q8LET2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8LET2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.249 (Depositor), 0.247 (DCC)
R-Value Work: 0.211 (Depositor), 0.211 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.572	α = 90
b = 82.572	β = 90
c = 86.847	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-04-01

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM118093

Revision History (Full details and data files)

Version 1.0: 2026-04-01
Type: Initial release

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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.