3U2R | pdb_00003u2r

Crystal structure of MarR transcription factor from Planctomyces limnophilus

PDB DOI: https://doi.org/10.2210/pdb3U2R/pdb

Classification: transcription regulator
Organism(s): Planctopirus limnophila DSM 3776
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-10-04 Released: 2011-10-19
Deposition Author(s): Michalska, K., Li, H., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.253 (Depositor), 0.251 (DCC)
R-Value Work:
0.201 (Depositor), 0.208 (DCC)
R-Value Observed:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of MarR transcription factor from Planctomyces limnophilus

Michalska, K., Li, H., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 19.9 kDa
Atom Count: 1,133
Modeled Residue Count: 135
Deposited Residue Count: 168
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Regulatory protein MarR	A	168	Planctopirus limnophila DSM 3776	Mutation(s): 0 Gene Names: Plim_0262
UniProt
Find proteins for D5SNV8 (Planctopirus limnophila (strain ATCC 43296 / DSM 3776 / IFAM 1008 / Mu 290)) Explore D5SNV8 Go to UniProtKB: D5SNV8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D5SNV8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	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: 0.253 (Depositor), 0.251 (DCC)
R-Value Work: 0.201 (Depositor), 0.208 (DCC)
R-Value Observed: 0.206 (Depositor)

Diffraction Data:

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.97	α = 90
b = 64.97	β = 90
c = 87.26	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELX	model building
MLPHARE	phasing
DM	model building
ARP/wARP	model building
Coot	model building
BUSTER	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
DM	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-10-19

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2011-10-19
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.