3E6M | pdb_00003e6m

The crystal structure of a MarR family transcriptional regulator from Silicibacter pomeroyi DSS.

PDB DOI: https://doi.org/10.2210/pdb3E6M/pdb

Classification: transcription regulator
Organism(s): Ruegeria pomeroyi
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-08-15 Released: 2008-09-02
Deposition Author(s): Tan, K., Volkart, L., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.230 (Depositor), 0.222 (DCC)
R-Value Work:
0.185 (Depositor), 0.185 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The crystal structure of a MarR family transcriptional regulator from Silicibacter pomeroyi DSS.

Tan, K., Volkart, L., Freeman, L., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 142.15 kDa
Atom Count: 9,532
Modeled Residue Count: 1,176
Deposited Residue Count: 1,288
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MarR family Transcriptional regulator	A, B, C, D, E A, B, C, D, E, F, G, H	161	Ruegeria pomeroyi	Mutation(s): 0 Gene Names: SPOA0451
UniProt
Find proteins for Q5LLB9 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LLB9 Go to UniProtKB: Q5LLB9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5LLB9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.230 (Depositor), 0.222 (DCC)
R-Value Work: 0.185 (Depositor), 0.185 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.433	α = 90
b = 93.198	β = 90.02
c = 101.556	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-09-02

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-09-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary

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.