3GP4

Crystal structure of putative MerR family transcriptional regulator from listeria monocytogenes

• PDB DOI: https://doi.org/10.2210/pdb3GP4/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Listeria monocytogenes serotype 4b str. F2365
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-20 Released: 2009-04-21 
• Deposition Author(s): Ramagopal, U.A., Toro, R., Morano, C., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.216 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Literature

Structure of putative MerR family transcriptional regulator from Listeria monocytogenes

Ramagopal, U.A., Toro, R., Morano, C., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.84 kDa 
• Atom Count: 2,450 
• Modelled Residue Count: 262 
• Deposited Residue Count: 284 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, MerR family	A, B	142	Listeria monocytogenes serotype 4b str. F2365	Mutation(s): 0  Gene Names: LMOf2365_2715

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MED	F [auth B]	D-METHIONINE C5 H11 N O2 S FFEARJCKVFRZRR-SCSAIBSYSA-N
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.216 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.647	α = 90
b = 80.647	β = 90
c = 127.126	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SHELXD	phasing
SHELXE	model building
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-21 
Deposition Author(s): Ramagopal, U.A., Toro, R., Morano, C., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-04-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references