6VLI | pdb_00006vli

Crystal structure of transcriptional regulator from bacteriophage 186

• PDB DOI: https://doi.org/10.2210/pdb6VLI/pdb

• Classification: GENE REGULATION
• Organism(s): Eganvirus ev186
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-01-24 Released: 2021-06-16 
• Deposition Author(s): Truong, J.Q., Panjikar, S., Bruning, J.B., Shearwin, K.E.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a transcriptional regulator from bacteriophage 186

Truong, J.Q., Pukala, T., Panjikar, S., Bruning, J.B., Shearwin, K.S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 74.27 kDa 
• Atom Count: 4,899 
• Modeled Residue Count: 594 
• Deposited Residue Count: 660 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Regulatory protein CII	A, B, C, D	165	Eganvirus ev186	Mutation(s): 0  Gene Names: CII, CP76
UniProt
Find proteins for P21678 (Escherichia phage 186) Explore P21678  Go to UniProtKB:  P21678

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIN	F [auth A]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
ACY	G [auth D]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
ACT	E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.47	α = 90
b = 53.51	β = 100.88
c = 106.35	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-06-16 
Deposition Author(s): Truong, J.Q., Panjikar, S., Bruning, J.B., Shearwin, K.E.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DP150103009
Australian Research Council (ARC)	Australia	DP160101450

Revision History  

• Version 1.0: 2021-06-16
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references
• Version 1.2: 2024-04-03
  Changes: Refinement description