Macromolecule Content

Total Structure Weight: 83.79 kDa
Atom Count: 5,832
Modelled Residue Count: 675
Deposited Residue Count: 717
Unique protein chains: 1

3BWG

The crystal structure of possible transcriptional regulator YydK from Bacillus subtilis subsp. subtilis str. 168

PDB DOI: https://doi.org/10.2210/pdb3BWG/pdb

Classification: TRANSCRIPTION REGULATOR
Organism(s): Bacillus subtilis subsp. subtilis str. 168
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2008-01-09 Released: 2008-01-22
Deposition Author(s): Tan, K., Zhou, M., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.228
R-Value Work: 0.186
R-Value Observed: 0.189

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The crystal structure of possible transcriptional regulator YydK from Bacillus subtilis subsp. subtilis str. 168.

Tan, K., Zhou, M., Abdullah, J., Joachimiak, A.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized HTH-type transcriptional regulator yydK	A, B, C	239	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0 Gene Names: yydK, BSU40130
UniProt
Find proteins for Q45591 (Bacillus subtilis (strain 168)) Explore Q45591 Go to UniProtKB: Q45591
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q45591
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C]	D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth C], K [auth C], L [auth C], M [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.228
R-Value Work: 0.186
R-Value Observed: 0.189
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.994	α = 90
b = 58.284	β = 110.08
c = 138.823	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
RESOLVE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-01-22

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-01-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance

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.