6DO0 | pdb_00006do0

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

• PDB DOI: https://doi.org/10.2210/pdb6DO0/pdb

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


• Deposited: 2018-06-08 Released: 2019-02-06 
• Deposition Author(s): Zadvornyy, O.A., Laureanti, J.A., Katipamula, S., O'Hagan, M., Peters, J.W.
• Funding Organization(s): Department of Energy (DOE, United States), Other government

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.323 (Depositor), 0.328 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.257 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

Protein Scaffold Activates Catalytic CO2 Hydrogenation by a Rhodium Bis(diphosphine) Complex

Laureanti, J.A., Buckho, G.W., Katipamula, S., Su, Q., Linehan, J.C., Zadvornyy, O.A., Peters, J.W., O'Hagan, M.

(2019) ACS Catal 9: 620-625

• DOI: https://doi.org/10.1021/acscatal.8b02615

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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 27.9 kDa 
• Atom Count: 1,753 
• Modeled Residue Count: 207 
• Deposited Residue Count: 234 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, PadR-like family	A, B	117	Lactococcus cremoris subsp. cremoris MG1363	Mutation(s): 3  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	C [auth A]	bis[diethyl(methyl)-lambda~5~-phosphanyl]{bis[{[(2-{[2-(2,5-dioxopyrrolidin-1-yl)ethyl]amino}-2-oxoethyl)amino]methyl}(diethyl)-lambda~5~-phosphanyl]}rhodium C36 H74 N6 O6 P4 Rh WBSWUPZUVFVXQZ-UHFFFAOYSA-R

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.323 (Depositor), 0.328 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.257 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.645	α = 90
b = 35.569	β = 96.51
c = 71.259	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-02-06 
Deposition Author(s): Zadvornyy, O.A., Laureanti, J.A., Katipamula, S., O'Hagan, M., Peters, J.W.

---

Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-SC0012518
Other government	United States	PNNL Laboratory Directed Research and Development 69937

Revision History  

• Version 1.0: 2019-02-06
  Type: Initial release
  
• Version 1.1: 2019-12-04
  Changes: Author supporting evidence
• Version 2.0: 2020-01-29
  Changes: Non-polymer description, Structure summary
• Version 2.1: 2020-09-02
  Changes: Database references, Derived calculations
• Version 2.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 2.3: 2024-10-30
  Changes: Structure summary