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

Validation slider image for 3E6M

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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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

View more in-depth experimental data

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 is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.