1YSQ | pdb_00001ysq

The crystal structure of transcriptional regulator YaiJ

• PDB DOI: https://doi.org/10.2210/pdb1YSQ/pdb

• Classification: GENE REGULATION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• 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., Edwards, A.M., Joachimiak, A., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.207 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.195 (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., Edwards, A.M., Savchenko, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.71 kDa 
• Atom Count: 1,552 
• Modeled Residue Count: 181 
• Deposited Residue Count: 193 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional regulator yiaJ	A	193	Escherichia coli	Mutation(s): 0  Gene Names: yiaJ
UniProt
Find proteins for P37671 (Escherichia coli (strain K12)) Explore P37671  Go to UniProtKB:  P37671

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A], C [auth A], D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.207 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.51	α = 90
b = 65.51	β = 90
c = 88.94	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
AMoRE	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., Edwards, A.M., 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: 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