2HZT

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.282 
• R-Value Work: 0.236 
• R-Value Observed: 0.236 

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

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

Macromolecules

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)) Go to UniProtKB:  O34533

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSU	A, B, C, D	L-PEPTIDE LINKING	C3 H7 N O5 S2		CYS
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 
• R-Value Work: 0.236 
• R-Value Observed: 0.236 
• 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

Entry History 

Deposition Data

• Released Date: 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)

Revision History  

• 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