4RK1

Crystal structure of LacI family transcriptional regulator from Enterococcus faecium, Target EFI-512930, with bound ribose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Crystal Structure of LacI Transcriptional Regulator Rbsr from Enterococcus faecium, Target EFI-512930

Patskovsky, Y.Toro, R.Bhosle, R.Al Obaidi, N.Chamala, S.Scott Glenn, A.Attonito, J.D.Chowdhury, S.Lafleur, J.Siedel, R.D.Hillerich, B.Love, J.Whalen, K.L.Gerlt, J.A.Almo, S.C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribose transcriptional regulatorA, B, C, D, E, F280Enterococcus faecium DOMutation(s): 0 
Gene Names: rbsRHMPREF0351_10453
UniProt
Find proteins for I3TZ89 (Enterococcus faecium (strain ATCC BAA-472 / TX0016 / DO))
Explore I3TZ89 
Go to UniProtKB:  I3TZ89
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RIB (Subject of Investigation/LOI)
Query on RIB

Download Ideal Coordinates CCD File 
BA [auth E], DA [auth F], G [auth A], K [auth B], Q [auth C], W [auth D]alpha-D-ribofuranose
C5 H10 O5
HMFHBZSHGGEWLO-AIHAYLRMSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth D] , CA [auth E] , EA [auth F] , FA [auth F] , GA [auth F] , H [auth A] , I [auth A] , J [auth A] , 
AA [auth D],  CA [auth E],  EA [auth F],  FA [auth F],  GA [auth F],  H [auth A],  I [auth A],  J [auth A],  L [auth B],  M [auth B],  N [auth B],  O [auth B],  P [auth B],  R [auth C],  S [auth C],  T [auth C],  U [auth C],  V [auth C],  X [auth D],  Y [auth D],  Z [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, FL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.371α = 90
b = 95.243β = 119.47
c = 123.602γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
ARP/wARPmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-29
    Type: Initial release
  • Version 1.1: 2015-02-18
    Changes: Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary