2HZT | pdb_00002hzt

Crystal Structure of a putative HTH-type transcriptional regulator ytcD

PDB DOI: https://doi.org/10.2210/pdb2HZT/pdb

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

Deposited: 2006-08-09 Released: 2006-08-29
Deposition Author(s): Madegowda, M., Eswaramoorthy, S., Desigan, K., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.282 (Depositor), 0.280 (DCC)
R-Value Work:
0.236 (Depositor), 0.230 (DCC)
R-Value Observed:
0.236 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal Structure of a putative HTH-type transcription regulator ytcD

Madegowda, M., Eswaramoorthy, S., Desigan, K., Burley, S.K., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 51.12 kDa
Atom Count: 3,369
Modeled Residue Count: 386
Deposited Residue Count: 428
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative HTH-type transcriptional regulator ytcD	A, B, C, D	107	Bacillus subtilis	Mutation(s): 0
UniProt
Find proteins for O34533 (Bacillus subtilis (strain 168)) Explore O34533 Go to UniProtKB: O34533
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O34533
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSU Query on CSU	A, B, C, D	L-PEPTIDE LINKING	C₃ H₇ N O₅ S₂		CYS
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.282 (Depositor), 0.280 (DCC)
R-Value Work: 0.236 (Depositor), 0.230 (DCC)
R-Value Observed: 0.236 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.273	α = 90
b = 45.521	β = 90
c = 230.276	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing
SHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-08-29

Deposition Author(s):

Eswaramoorthy, S.

Swaminathan, S.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2006-08-29
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2012-12-05
Changes: Database references
Version 1.4: 2017-09-13
Changes: Refinement description
Version 1.5: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.6: 2025-03-26
Changes: Data collection, Database references, Structure summary

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.