4JYK | pdb_00004jyk

Structure of E. coli Transcriptional Regulator RutR with bound uracil

• PDB DOI: https://doi.org/10.2210/pdb4JYK/pdb

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


• Deposited: 2013-03-29 Released: 2013-08-14 
• Deposition Author(s): Cooper, D.R., Knapik, A.A., Petkowski, J.J., Porebski, P.J., Osinski, T., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.170 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.120 (Depositor), 0.134 (DCC) 
• R-Value Observed: 
  0.122 (Depositor) 

Literature

Structure of E. coli Transcriptional Regulator RutR with bound uracil

Cooper, D.R., Knapik, A.A., Petkowski, J.J., Porebski, P.J., Osinski, T., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

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: 48.33 kDa 
• Atom Count: 3,504 
• Modeled Residue Count: 397 
• Deposited Residue Count: 424 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
URA	G [auth A], K [auth B]	URACIL C4 H4 N2 O2 ISAKRJDGNUQOIC-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.170 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.120 (Depositor), 0.134 (DCC) 
• R-Value Observed: 0.122 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33S3X

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.15	α = 90
b = 86.14	β = 106.23
c = 69.019	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-14 
Deposition Author(s): Cooper, D.R., Knapik, A.A., Petkowski, J.J., Porebski, P.J., Osinski, T., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2013-08-14
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-02-28
  Changes: Data collection, Refinement description