2QSJ

Crystal structure of a LuxR family DNA-binding response regulator from Silicibacter pomeroyi

PDB DOI: https://doi.org/10.2210/pdb2QSJ/pdb

Classification: TRANSCRIPTION
Organism(s): Ruegeria pomeroyi DSS-3
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-07-31 Released: 2007-08-14
Deposition Author(s): Bonanno, J.B., Freeman, J., Bain, K.T., Mendoza, M., Romero, R., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.267
R-Value Work: 0.228
R-Value Observed: 0.230

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of a LuxR family DNA-binding response regulator from Silicibacter pomeroyi.

Bonanno, J.B., Freeman, J., Bain, K.T., Mendoza, M., Romero, R., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 33.14 kDa
Atom Count: 1,854
Modelled Residue Count: 242
Deposited Residue Count: 308
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding response regulator, LuxR family	A, B	154	Ruegeria pomeroyi DSS-3	Mutation(s): 0 Gene Names: SPO2369
UniProt
Find proteins for Q5LQW4 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LQW4 Go to UniProtKB: Q5LQW4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5LQW4
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.267
R-Value Work: 0.228
R-Value Observed: 0.230
Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.459	α = 90
b = 57.459	β = 90
c = 111.354	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-08-14

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2007-08-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2018-11-14
Changes: Data collection, Structure summary
Version 1.4: 2021-02-03
Changes: Database references, Structure summary
Version 1.5: 2024-02-21
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.