6VWE | pdb_00006vwe

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.280 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.213 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted JY1Click on this verticalbar to view details

This is version 1.4 of the entry. See complete history


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 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulator, PadR-like family
A, B
119Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 4 
Gene Names: llmg_0323
UniProt
Find proteins for A2RI36 (Lactococcus lactis subsp. cremoris (strain MG1363))
Explore A2RI36 
Go to UniProtKB:  A2RI36
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2RI36
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JY1 (Subject of Investigation/LOI)
Query on JY1

Download Ideal Coordinates CCD File 
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: 2.50 Å
  • R-Value Free:  0.280 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.213 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.855α = 90
b = 35.619β = 95.92
c = 71.651γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted JY1Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-FG02-04ER151563
Department of Energy (DOE, United States)United StatesDE-AC02-76SF00515
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103393

Revision History  (Full details and data files)

  • 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