6Z1B | pdb_00006z1b

Structure of K52-acetylated RutR in complex with uracil.

• PDB DOI: https://doi.org/10.2210/pdb6Z1B/pdb

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


• Deposited: 2020-05-13 Released: 2022-06-01 
• Deposition Author(s): Kremer, M., Schulze, S., Lammers, M.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.215 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Structure of K52-acetylated RutR in complex with uracil.

Kremer, M., Schulze, S., Baumann, U.

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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 49.96 kDa 
• Atom Count: 3,455 
• Modeled Residue Count: 403 
• Deposited Residue Count: 440 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional regulator RutR	A, B	220	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
URA	C [auth A], G [auth B]	URACIL C4 H4 N2 O2 ISAKRJDGNUQOIC-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	A, B	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.215 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.307	α = 90
b = 88.547	β = 90
c = 150.004	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-01 
Deposition Author(s): Kremer, M., Schulze, S., Lammers, M.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	LA 2984/5

Revision History  

• Version 1.0: 2022-06-01
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Refinement description
• Version 2.1: 2024-01-24
  Changes: Refinement description
• Version 2.2: 2024-10-09
  Changes: Structure summary