2QSJ | pdb_00002qsj

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 (Depositor), 0.263 (DCC)
R-Value Work:
0.228 (Depositor), 0.225 (DCC)
R-Value Observed:
0.230 (Depositor)

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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
Modeled Residue Count: 242
Deposited Residue Count: 308
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 (Depositor), 0.263 (DCC)
R-Value Work: 0.228 (Depositor), 0.225 (DCC)
R-Value Observed: 0.230 (Depositor)

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

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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