7V5V | pdb_00007v5v

LysR family transcriptional regulator RipR from Salmonella Typhimurium

PDB DOI: https://doi.org/10.2210/pdb7V5V/pdb

Classification: TRANSCRIPTION
Organism(s): Salmonella enterica subsp. enterica serovar Enteritidis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-08-18 Released: 2022-08-24
Deposition Author(s): Ki, N., Ha, N.-C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free:
0.295 (Depositor), 0.288 (DCC)
R-Value Work:
0.236 (Depositor), 0.235 (DCC)
R-Value Observed:
0.238 (Depositor)

Starting Model: in silico
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This is version 1.1 of the entry. See complete history.

Literature

The activation mechanism of the itaconic acid-responsive LTTR RipR in the pathogenesis of the foodborne-pathogen Salmonella enterica

Ki, N.

To be published.

Macromolecule Content

Total Structure Weight: 90.55 kDa
Atom Count: 6,309
Modeled Residue Count: 822
Deposited Residue Count: 832
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RipR	A, B, C, D	208	Salmonella enterica subsp. enterica serovar Enteritidis	Mutation(s): 0 Gene Names: stmR
UniProt
Find proteins for H9L457 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore H9L457 Go to UniProtKB: H9L457
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	H9L457
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free: 0.295 (Depositor), 0.288 (DCC)
R-Value Work: 0.236 (Depositor), 0.235 (DCC)
R-Value Observed: 0.238 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.405	α = 90
b = 72.415	β = 104.62
c = 91.612	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-08-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-08-24
Type: Initial release
Version 1.1: 2024-04-03
Changes: Data collection, Refinement description

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.