2D1V

Crystal structure of DNA-binding domain of Bacillus subtilis YycF

PDB DOI: https://doi.org/10.2210/pdb2D1V/pdb

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

Deposited: 2005-09-01 Released: 2006-09-12
Deposition Author(s): Okajima, T., Okada, A., Watanabe, T., Yamamoto, K., Tanizawa, K., Utsumi, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.232
R-Value Work: 0.228
R-Value Observed: 0.229

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Response regulator YycF essential for bacterial growth: X-ray crystal structure of the DNA-binding domain and its PhoB-like DNA recognition motif

Okajima, T., Doi, A., Okada, A., Gotoh, Y., Tanizawa, K., Utsumi, R.

(2008) FEBS Lett 582: 3434-3438

PubMed: 18789936 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2008.09.007
Primary Citation of Related Structures:
2D1V

PubMed Abstract:
A response regulator YycF and its cognate sensor kinase YycG constitute the two-component signal transduction system essential for growth of Gram-positive bacteria with a low GC content. We have determined the X-ray crystal structure of the effector domain of Bacillus subtilis YycF involved in DNA binding. The structure, containing a winged helix-turn-helix motif, was found to be very similar to that of the response regulator PhoB from Escherichia coli. Specific binding of YycF to the PhoB-regulated alkaline phosphatase promoter was also demonstrated.

Organizational Affiliation

Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan. tokajima@sanken.osaka-u.ac.jp

Macromolecule Content

Total Structure Weight: 12.81 kDa
Atom Count: 901
Modelled Residue Count: 103
Deposited Residue Count: 108
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulatory protein yycF	A	108	Bacillus subtilis	Mutation(s): 0 Gene Names: yycF
UniProt
Find proteins for P37478 (Bacillus subtilis (strain 168)) Explore P37478 Go to UniProtKB: P37478
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P37478
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.232
R-Value Work: 0.228
R-Value Observed: 0.229
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.754	α = 90
b = 65.584	β = 90
c = 79.07	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-09-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-09-12
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2024-03-13
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.