4R9N | pdb_00004r9n

DeoR family transcriptional regulator from Listeria monocytogenes.

• PDB DOI: https://doi.org/10.2210/pdb4R9N/pdb

• Classification: TRANSCRIPTION
• Organism(s): Listeria monocytogenes EGD-e
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-09-05 Released: 2014-09-17 
• Deposition Author(s): Osipiuk, J., Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.231 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

DeoR family transcriptional regulator from Listeria monocytogenes.

Osipiuk, J., Wu, R., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.61 kDa 
• Atom Count: 2,195 
• Modeled Residue Count: 247 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lmo0547 protein	A	254	Listeria monocytogenes EGD-e	Mutation(s): 0  Gene Names: lmo0547
UniProt
Find proteins for Q8Y9I1 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y9I1  Go to UniProtKB:  Q8Y9I1

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.231 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34R9N

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.818	α = 90
b = 52.818	β = 90
c = 172.283	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXCD	phasing
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-17 
Deposition Author(s): Osipiuk, J., Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2014-09-17
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary