6VWE | pdb_00006vwe

Crystal structure of the D100R multidrug binding transcriptional regulator LmrR in complex with Rhodium Bis-diphosphine Complex

• PDB DOI: https://doi.org/10.2210/pdb6VWE/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Lactococcus cremoris subsp. cremoris MG1363
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-02-19 Released: 2020-04-01 
• Deposition Author(s): Zadvornyy, O.A., Laureanti, J.A., Peters, J.W.
• Funding Organization(s): Department of Energy (DOE, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.280 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

A Positive Charge in the Outer Coordination Sphere of an Artificial Enzyme Increases CO2 Hydrogenation

Laureanti, J.A., Ginovska, B., Buchko, G.W., Schenter, G.K., Zadvornyy, O.A., Heberta, M., Peters, J.W., Shaw, W.J.

(2020) Organometallics 

• DOI: https://doi.org/10.1021/acs.organomet.9b00843

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.27 kDa 
• Atom Count: 1,753 
• Modeled Residue Count: 207 
• Deposited Residue Count: 238 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, PadR-like family	A, B	119	Lactococcus cremoris subsp. cremoris MG1363	Mutation(s): 4  Gene Names: llmg_0323
UniProt
Find proteins for A2RI36 (Lactococcus lactis subsp. cremoris (strain MG1363)) Explore A2RI36  Go to UniProtKB:  A2RI36

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JY1 (Subject of Investigation/LOI)	C [auth A]	bis{N~2~,N~2~-bis[(diethylphosphanuidyl-kappaP)methyl]-N-[2-(2,5-dioxopyrrolidin-1-yl)ethyl]glycinamide}rhodium C36 H70 N6 O6 P4 Rh KIKWETXGDLBDBZ-UHFFFAOYSA-R

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.280 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.855	α = 90
b = 35.619	β = 95.92
c = 71.651	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-04-01 
Deposition Author(s): Zadvornyy, O.A., Laureanti, J.A., Peters, J.W.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-FG02-04ER151563
Department of Energy (DOE, United States)	United States	DE-AC02-76SF00515
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41GM103393

Revision History  

• Version 1.0: 2020-04-01
  Type: Initial release
  
• Version 1.1: 2023-02-08
  Changes: Advisory, Database references
• Version 1.2: 2023-10-04
  Changes: Data collection
• Version 1.3: 2023-10-25
  Changes: Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary
• Version 2.0: 2026-08-12
  Type: Remediation
  Reason: Metalloprotein remediation
  Changes: Data collection, Derived calculations, Non-polymer description, Structure summary