9KPR | pdb_00009kpr

Crystal structure of a allulose transcriptional regulator from Agrobacterium fabrum

PDB DOI: https://doi.org/10.2210/pdb9KPR/pdb

Classification: TRANSCRIPTION
Organism(s): Agrobacterium fabrum str. C58
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2024-11-24 Released: 2025-11-26
Deposition Author(s): Wei, H.L., Dong, Q.Z., Liu, W.D., Yang, J.G., Sun, Y.X.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free:
0.261 (Depositor), 0.259 (DCC)
R-Value Work:
0.231 (Depositor), 0.234 (DCC)

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

Ligand Structure Quality Assessment

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

Literature

Crystal structure of a allulose transcriptional regulator from Agrobacterium fabrum

Wei, H.L., Dong, Q.Z., Liu, W.D., Yang, J.G., Sun, Y.X.

To be published.

Macromolecule Content

Total Structure Weight: 79.37 kDa
Atom Count: 4,585
Modeled Residue Count: 567
Deposited Residue Count: 718
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, LacI family	A, B	359	Agrobacterium fabrum str. C58	Mutation(s): 0 Gene Names: Atu4743
UniProt
Find proteins for A9CH24 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CH24 Go to UniProtKB: A9CH24
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9CH24
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EGE (Subject of Investigation/LOI) Query on A1EGE Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	D-Allulose C₆ H₁₂ O₆ LKDRXBCSQODPBY-KVTDHHQDSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free: 0.261 (Depositor), 0.259 (DCC)
R-Value Work: 0.231 (Depositor), 0.234 (DCC)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.109	α = 90
b = 113.109	β = 90
c = 210.058	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-26

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-11-26
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.