3HFU | pdb_00003hfu

Crystal structure of the ligand binding domain of E. coli CynR with its specific effector azide

• PDB DOI: https://doi.org/10.2210/pdb3HFU/pdb

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-12 Released: 2009-06-09 
• Deposition Author(s): Singer, A.U., Evdokimova, E., Kagan, O., Dong, A., Edwards, A.M., Savchenko, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.274 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.227 (DCC) 

Starting Model: experimental

Literature

Crystal structure of the ligand binding domain of E. coli CynR with its specific effector azide

Singer, A.U., Evdokimova, E., Kagan, O., Cuff, M.E., Edwards, A.M., Joachimiak, A., Savchenko, A.

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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 105.92 kDa 
• Atom Count: 6,782 
• Modeled Residue Count: 811 
• Deposited Residue Count: 952 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional regulator cynR	A, B, C, D	238	Escherichia coli K-12	Mutation(s): 0  Gene Names: b0338, cynR, JW5894
UniProt
Find proteins for P27111 (Escherichia coli (strain K12)) Explore P27111  Go to UniProtKB:  P27111

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	H [auth C], J [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
AZI	E [auth A], F [auth B], G [auth C], I [auth D]	AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.274 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.227 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.176	α = 90
b = 98.363	β = 103.769
c = 86.272	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-09 
Deposition Author(s): Singer, A.U., Evdokimova, E., Kagan, O., Dong, A., Edwards, A.M., Savchenko, A.

Revision History  

• Version 1.0: 2009-06-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-22
  Changes: Data collection
• Version 1.4: 2024-11-27
  Changes: Structure summary