7Q34 | pdb_00007q34

Crystal structure of the multidrug binding transcriptional regulator LmrR in complex squaraine dye

• PDB DOI: https://doi.org/10.2210/pdb7Q34/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Lactococcus lactis subsp. lactis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-10-26 Released: 2022-06-01 
• Deposition Author(s): Liutkus, M., Mejias, S.H., Barolo, C., Cortajarena, A.L.
• Funding Organization(s): European Union (EU), European Research Council (ERC), Spanish National Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.317 (Depositor), 0.312 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.245 (DCC) 
• R-Value Observed: 
  0.244 (Depositor) 

Starting Model: experimental

Literature

Designing Artificial Fluorescent Proteins: Squaraine-LmrR Biophosphors for High Performance Deep-Red Biohybrid Light-Emitting Diodes

Ferrara, S., Mejias, S.H., Liutkus, M., Renno, G., Stella, F., Kociolek, I., Fuenzalida-Werner, J.P., Barolo, C., Coto, P.B., Cortajarena, A.L., Costa, R.D.

(2022) Adv Funct Mater 32: 2111381

• DOI: https://doi.org/10.1002/adfm.202111381

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 60.71 kDa 
• Atom Count: 3,252 
• Modeled Residue Count: 392 
• Deposited Residue Count: 528 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Helix-turn-helix transcriptional regulator	A, B, C, D	132	Lactococcus lactis subsp. lactis	Mutation(s): 0  Gene Names:  CYU10_001323, D4M07_02500, E34_1323, FEZ45_05535, FIB48_07105, GJI88_04795, HPC60_09780, JCM5805K_2657, KF282_0527, LKF24_1179, LKF67_0238, LL14B4_01620, LL275_0346, LLUC06_0422, LLUC08_0288, LLUC11_0290, LMG8520_0357, LMG9449_1101, N42_0245, VN91_0116
UniProt
Find proteins for A0A0A7SZD7 (Lactococcus lactis subsp. lactis) Explore A0A0A7SZD7  Go to UniProtKB:  A0A0A7SZD7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8TF (Subject of Investigation/LOI)	G [auth A], J [auth C]	2,4-bis[(E)-(1-ethyl-3,3-dimethyl-indol-2-ylidene)methyl]cyclobutane-1,3-dione C30 H34 N2 O2 RFXRJJSGFNDERY-FAKNRSBRSA-N
NI	E [auth A], F [auth A], H [auth B], I [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.317 (Depositor), 0.312 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.245 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.658	α = 90
b = 68.019	β = 90
c = 200.858	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-01 
Deposition Author(s): Liutkus, M., Mejias, S.H., Barolo, C., Cortajarena, A.L.

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Funding Organization	Location	Grant Number
European Union (EU)	Spain	863170
European Research Council (ERC)	Spain	ERC-CoG-648071-ProNANO
Spanish National Research Council	Spain	PID2019-111649RB-I00

Revision History  

• Version 1.0: 2022-06-01
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description