9KKD | pdb_00009kkd

the structure of StnY

PDB DOI: https://doi.org/10.2210/pdb9KKD/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Streptomyces albus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-11-13 Released: 2025-11-19
Deposition Author(s): Yang, S.Q., Guo, W.L., Yang, X., Liang, R.B., Huang, T.T., Fan, C.P., Zheng, J.T., Lin, S.J.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.255 (Depositor), 0.268 (DCC)
R-Value Work:
0.208 (Depositor), 0.221 (DCC)
R-Value Observed:
0.211 (Depositor)

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

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

Literature

RHH family transcription factor serves as molecular switch of antibiotics resistance operon coupling of drug efflux pump and drug binding protein

Yang, S.Q., Guo, W.L., Yang, X., Liang, R.B., Huang, T.T., Fan, C.P., Zheng, J.T., Lin, S.J.

To be published.

Macromolecule Content

Total Structure Weight: 29.06 kDa
Atom Count: 1,501
Modeled Residue Count: 176
Deposited Residue Count: 240
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribbon-helix-helix protein, CopG family	A, B, C, D	60	Streptomyces albus	Mutation(s): 0 Gene Names: D8771_34895
UniProt
Find proteins for A0A6C1BW07 (Streptomyces albus) Explore A0A6C1BW07 Go to UniProtKB: A0A6C1BW07
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6C1BW07
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.255 (Depositor), 0.268 (DCC)
R-Value Work: 0.208 (Depositor), 0.221 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.706	α = 90
b = 53.626	β = 90
c = 103.937	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
PHASER	phasing
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2023YFA0914200

Revision History (Full details and data files)

Version 1.0: 2025-11-19
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.