7VIM | pdb_00007vim

The C-terminal DNA binding domain of EsrB from Edwardsiella piscicida

• PDB DOI: https://doi.org/10.2210/pdb7VIM/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Edwardsiella piscicida
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2021-09-27 Released: 2022-09-28 
• Deposition Author(s): Liu, B., Reverter, D., Shao, S.
• Funding Organization(s): Spanish Ministry of Economy and Competitiveness

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.281 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.229 (Depositor) 
• R-Value Observed: 
  0.232 (Depositor) 

Literature

The C-terminal DNA binding domain of EsrB from Edwardsiella piscicida

Liu, B., Reverter, D., Shao, 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: 16.56 kDa 
• Atom Count: 1,077 
• Modeled Residue Count: 131 
• Deposited Residue Count: 144 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein EsrB	A, B	72	Edwardsiella piscicida	Mutation(s): 0  Gene Names: EVK84_02890, MA13_contig00007-0127

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.281 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.229 (Depositor) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.111	α = 90
b = 58.051	β = 90
c = 81.043	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-09-28 
Deposition Author(s): Liu, B., Reverter, D., Shao, S.

---

Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	BFU2015-66417-P (MINECO/FEDER)

Revision History  

• Version 1.0: 2022-09-28
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection