9X3C | pdb_00009x3c

Crystal structure of B. subtilis YdzF in reduced state

PDB DOI: https://doi.org/10.2210/pdb9X3C/pdb

Classification: TRANSCRIPTION
Organism(s): Bacillus subtilis PY79
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-10-09 Released: 2026-09-09
Deposition Author(s): Barman, R., Baidya, A.K.
Funding Organization(s): Department of Biotechnology (DBT, India), Science and Engineering Research Board (SERB)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.54 Å
R-Value Free:
0.308 (Depositor), 0.312 (DCC)
R-Value Work:
0.243 (Depositor), 0.245 (DCC)

Starting Model: in silico
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This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of B. subtilis YdzF in reduced state

Barman, R., Baidya, A.K.

To be published.

Macromolecule Content

Total Structure Weight: 54.64 kDa
Atom Count: 2,849
Modeled Residue Count: 367
Deposited Residue Count: 472
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized HTH-type transcriptional regulator YdzF	A, B [auth C], C [auth B], D	118	Bacillus subtilis PY79	Mutation(s): 0 Gene Names: ydzF, BSU05270
UniProt
Find proteins for O31494 (Bacillus subtilis (strain 168)) Explore O31494 Go to UniProtKB: O31494
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O31494
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.54 Å
R-Value Free: 0.308 (Depositor), 0.312 (DCC)
R-Value Work: 0.243 (Depositor), 0.245 (DCC)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.07	α = 90
b = 119.03	β = 90
c = 79.92	γ = 90

Software Package:

Software Name	Purpose
Coot	model building
REFMAC	refinement
PHASER	phasing
Aimless	data scaling
iMOSFLM	data reduction
MAR345dtb	data collection

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	BT/RLF/Re-entry/71/2020
Science and Engineering Research Board (SERB)	India	EEQ/2021/000834

Revision History (Full details and data files)

Version 1.0: 2026-09-09
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.