6NDI | pdb_00006ndi

Crystal Structure of the Sugar Binding Domain of LacI Family Protein from Klebsiella pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.235 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae.

Inniss, N.L.Kochan, T.J.Minasov, G.Wawrzak, Z.Chang, C.Tan, K.Shuvalova, L.Kiryukhina, O.Pshenychnyi, S.Wu, R.Dubrovska, I.Babnigg, G.Endres, M.Anderson, W.F.Hauser, A.R.Joachimiak, A.Satchell, K.J.F.

(2023) Microbiol Resour Announc 12: e0101322-e0101322

  • DOI: https://doi.org/10.1128/mra.01013-22
  • Primary Citation of Related Structures:  
    6DT3, 6DUX, 6DVV, 6DXN, 6E85, 6NAU, 6NBG, 6NDI, 6WN5, 6WN8, 6X1L, 7RJJ, 7TL5, 7TZP

  • PubMed Abstract: 

    Klebsiella pneumoniae is a leading cause of antibiotic-resistant-associated deaths in the world. Here, we report the deposition of 14 structures of enzymes from both the core and accessory genomes of sequence type 23 (ST23) K1 hypervirulent K. pneumoniae.


  • Organizational Affiliation
    • Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulator
A, B
334Klebsiella pneumoniae subsp. pneumoniaeMutation(s): 0 
Gene Names: AN676_0312450
UniProt
Find proteins for A0A2W0LW10 (Klebsiella pneumoniae subsp. pneumoniae)
Explore A0A2W0LW10 
Go to UniProtKB:  A0A2W0LW10
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2W0LW10
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.235 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.737α = 90
b = 110.478β = 97.94
c = 37.777γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-26
    Type: Initial release
  • Version 1.1: 2022-11-30
    Changes: Database references, Structure summary
  • Version 1.2: 2023-06-14
    Changes: Database references, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Data collection, Structure summary