6CHK

Crystal structure of LacI family transcriptional regulator from Lactobacillus casei, Target EFI-512911, with bound TRIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Automatic recognition of ligands in electron density by machine learning.

Kowiel, M.Brzezinski, D.Porebski, P.J.Shabalin, I.G.Jaskolski, M.Minor, W.

(2019) Bioinformatics 35: 452-461

  • DOI: 10.1093/bioinformatics/bty626
  • Primary Citation of Related Structures:  
    6CHK

  • PubMed Abstract: 
  • The correct identification of ligands in crystal structures of protein complexes is the cornerstone of structure-guided drug design. However, cognitive bias can sometimes mislead investigators into modeling fictitious compounds without solid support from the electron density maps ...

    The correct identification of ligands in crystal structures of protein complexes is the cornerstone of structure-guided drug design. However, cognitive bias can sometimes mislead investigators into modeling fictitious compounds without solid support from the electron density maps. Ligand identification can be aided by automatic methods, but existing approaches are based on time-consuming iterative fitting.


    Organizational Affiliation

    Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, VA, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcriptional regulator, LacI familyA282Lactobacillus paracasei ATCC 334Mutation(s): 0 
Gene Names: LSEI_2103
Find proteins for Q036L9 (Lactobacillus paracasei (strain ATCC 334 / BCRC 17002 / CIP 107868 / KCTC 3260 / NRRL B-441))
Explore Q036L9 
Go to UniProtKB:  Q036L9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download Ideal Coordinates CCD File 
B [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.715α = 90
b = 108.715β = 90
c = 125.395γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SHELXphasing
SHELXmodel building
ARP/wARPmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesHG008424
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM117325
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM117080

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2018-10-17
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2018-12-26
    Changes: Data collection, Database references
  • Version 1.3: 2019-02-20
    Changes: Author supporting evidence, Data collection, Database references
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence, Database references