1YSP

Crystal structure of the C-terminal domain of E. coli transcriptional regulator KdgR.

• PDB DOI: https://doi.org/10.2210/pdb1YSP/pdb

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-02-08 Released: 2005-03-22 
• Deposition Author(s): Bochkarev, A., Lunin, V.V., Ezersky, A., Evdokimova, E., Skarina, T., Xu, X., Borek, D., Joachimiak, A., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.259 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

Structural study of effector binding specificity in IclR transcriptional regulators

Bochkarev, A., Lunin, V.V., Ezersky, A., Evdokimova, E., Skarina, T., Xu, X., Borek, D., Savchenko, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 20.94 kDa 
• Atom Count: 1,535 
• Modelled Residue Count: 164 
• Deposited Residue Count: 181 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator kdgR	A	181	Escherichia coli	Mutation(s): 0  Gene Names: kdgR
UniProt
Find proteins for P76268 (Escherichia coli (strain K12)) Explore P76268  Go to UniProtKB:  P76268

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.259 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.54	α = 90
b = 31.54	β = 92.7
c = 37.05	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-22 
Deposition Author(s): Bochkarev, A., Lunin, V.V., Ezersky, A., Evdokimova, E., Skarina, T., Xu, X., Borek, D., Joachimiak, A., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2005-03-22
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2011-10-05
  Changes: Structure summary
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations