5U93 | pdb_00005u93

Structure of the Regulatory Domain of the AraC Family Transcriptional Activator RhaR

• PDB DOI: https://doi.org/10.2210/pdb5U93/pdb

• Classification: TRANSCRIPTION
• Organism(s): Bacteria Latreille et al. 1825
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-12-15 Released: 2017-12-20 
• Deposition Author(s): Zhao, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.203 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.171 (Depositor) 
• R-Value Observed: 
  0.172 (Depositor) 

Literature

Structure of the Regulatory Domain of the AraC Family Transcriptional Activator RhaR

Lin, J., Zhao, H., Shaath, D., Wehmeye, G., Kolin, A., Egan, 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)

Macromolecule Content 

• Total Structure Weight: 40.24 kDa 
• Atom Count: 2,812 
• Modeled Residue Count: 321 
• Deposited Residue Count: 344 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional activator RhaR	A, B	172	Bacteria Latreille et al. 1825	Mutation(s): 0
UniProt
Find proteins for P09378 (Escherichia coli (strain K12)) Explore P09378  Go to UniProtKB:  P09378

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RM4	D [auth A], F [auth B]	beta-L-rhamnopyranose C6 H12 O5 SHZGCJCMOBCMKK-YJRYQGEOSA-N
NI	C [auth A], E [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	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:  0.203 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.171 (Depositor) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.793	α = 90
b = 100.793	β = 90
c = 95.696	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): Zhao, H.

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Structure summary