4XK4 | pdb_00004xk4

E. coli transcriptional regulator RUTR with dihydrouracil

• PDB DOI: https://doi.org/10.2210/pdb4XK4/pdb

• Classification: Transcription Regulator
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-01-09 Released: 2015-05-13 
• Deposition Author(s): Shumilin, I.A., Cooper, D.R., Shabalin, I.G., Grabowski, M., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 
  0.225 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

E. COLI TRANSCRIPTIONAL REGULATOR RUTR WITH DIHYDROURACIL

Minor, W.

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: 95.32 kDa 
• Atom Count: 6,403 
• Modeled Residue Count: 787 
• Deposited Residue Count: 848 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional regulator RutR	A, B, C, D	212	Escherichia coli K-12	Mutation(s): 0  Gene Names: rutR, ycdC, b1013, JW0998
UniProt
Find proteins for P0ACU2 (Escherichia coli (strain K12)) Explore P0ACU2  Go to UniProtKB:  P0ACU2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DUC	E [auth A], F [auth B], G [auth C], H [auth D]	DIHYDROPYRIMIDINE-2,4(1H,3H)-DIONE C4 H6 N2 O2 OIVLITBTBDPEFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free:  0.225 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.892	α = 88.37
b = 55.672	β = 88.8
c = 85.242	γ = 62.37

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
PDB_EXTRACT	data extraction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-05-13 
Deposition Author(s): Shumilin, I.A., Cooper, D.R., Shabalin, I.G., Grabowski, M., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	NIH-5U54GM094662

Revision History  

• Version 1.0: 2015-05-13
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2022-04-13
  Changes: Database references, Structure summary
• Version 1.4: 2023-09-27
  Changes: Data collection, Refinement description