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), 0.270 (DCC)
R-Value Work:
0.229 (Depositor), 0.230 (DCC)
R-Value Observed:
0.232 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

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

Liu, B., Reverter, D., Shao, S.

To be published.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.281 (Depositor), 0.270 (DCC)
R-Value Work: 0.229 (Depositor), 0.230 (DCC)
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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-09-28

Deposition Author(s):

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

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.