9L2H | pdb_00009l2h

Crystal structure of AnAE-N267D mutant in complex with paraoxon

PDB DOI: https://doi.org/10.2210/pdb9L2H/pdb

Classification: HYDROLASE
Organism(s): Aspergillus niger
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-12-17 Released: 2025-10-29
Deposition Author(s): Xing, S.Q., Hu, G.L., He, L.P.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free:
0.167 (Depositor), 0.167 (DCC)
R-Value Work:
0.145 (Depositor), 0.146 (DCC)
R-Value Observed:
0.146 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural and Functional Characterization of a Novel GDSL-Acetylesterase from Aspergillus niger Reveals Unique Acylated Choline Specificity

Xing, S.Q., Hu, G.L., Xie, W., Wang, L., Tian, G.H., Yuan, Y., Gao, F.L., Wang, X., Li, C.Q., He, L.P.

To be published.

Macromolecule Content

Total Structure Weight: 32.62 kDa
Atom Count: 2,515
Modeled Residue Count: 270
Deposited Residue Count: 293
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellulose-binding GDSL lipase/acylhydrolase	A	293	Aspergillus niger	Mutation(s): 1 Gene Names: CAN33_0018055 EC: 3.1.1.7
UniProt
Find proteins for A0A254UBZ6 (Aspergillus niger) Explore A0A254UBZ6 Go to UniProtKB: A0A254UBZ6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A254UBZ6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DPF (Subject of Investigation/LOI) Query on DPF 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]	DIETHYL HYDROGEN PHOSPHATE C₄ H₁₁ O₄ P UCQFCFPECQILOL-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-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: 1.71 Å
R-Value Free: 0.167 (Depositor), 0.167 (DCC)
R-Value Work: 0.145 (Depositor), 0.146 (DCC)
R-Value Observed: 0.146 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.722	α = 90
b = 78.722	β = 90
c = 91.659	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-29

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31870002

Revision History (Full details and data files)

Version 1.0: 2025-10-29
Type: Initial release
Version 1.1: 2025-11-05
Changes: Database references, Structure summary

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.