9M2Y | pdb_00009m2y

Crystal structure of a DUF3237 protein from Aspergillus

PDB DOI: https://doi.org/10.2210/pdb9M2Y/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Aspergillus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-02-28 Released: 2025-04-09
Deposition Author(s): Li, C.P., Xiao, Q.J., Yang, M.H.
Funding Organization(s): Ministry of Education (MoE, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free:
0.190 (Depositor), 0.190 (DCC)
R-Value Work:
0.173 (Depositor), 0.173 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure and proposed mechanism of a DUF3237 protein from Aspergillus.

Li, C.P., Fu, Y.Z., Jiang, Q.Y., Zhu, L.J., Gu, L., Yang, M.H., Kong, L.Y.

To be published.

Macromolecule Content

Total Structure Weight: 16.98 kDa
Atom Count: 1,076
Modeled Residue Count: 127
Deposited Residue Count: 157
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF3237 protein	A	157	Aspergillus	Mutation(s): 0
UniProt
Find proteins for A0A1L9TCT0 (Aspergillus sydowii CBS 593.65) Explore A0A1L9TCT0 Go to UniProtKB: A0A1L9TCT0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1L9TCT0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EMO (Subject of Investigation/LOI) Query on A1EMO 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]	6-[(2E,4E,6E)-6-methylocta-2,4,6-trien-2-yl]-4-oxidanyl-pyran-2-one C₁₄ H₁₆ O₃ XLEKERYMFDYNQR-DTBWVNQVSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free: 0.190 (Depositor), 0.190 (DCC)
R-Value Work: 0.173 (Depositor), 0.173 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.36	α = 90
b = 70.911	β = 90
c = 90.204	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Education (MoE, China)	China	B18056

Revision History (Full details and data files)

Version 1.0: 2025-04-09
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.