6NDI

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

• PDB DOI: https://doi.org/10.2210/pdb6NDI/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Klebsiella pneumoniae subsp. pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-12-13 Released: 2018-12-26 
• Deposition Author(s): Minasov, G., Shuvalova, L., Wawrzak, Z., Kiryukhina, O., Dubrovska, I., Anderson, W.F., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.235 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

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

• PubMed: 36695589 
• 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.

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Organizational Affiliation: 

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

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)

Macromolecule Content

• Total Structure Weight: 73.88 kDa 
• Atom Count: 4,373 
• Modelled Residue Count: 544 
• Deposited Residue Count: 668 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator	A, B	334	Klebsiella pneumoniae subsp. pneumoniae	Mutation(s): 0  Gene Names: AN676_0312450
UniProt
Find proteins for A0A2W0LW10 (Klebsiella pneumoniae subsp. pneumoniae) Explore A0A2W0LW10  Go to UniProtKB:  A0A2W0LW10

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.235 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: C 1 2 1
• Diffraction Data: https://doi.org/10.18430/m36ndi

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.737	α = 90
b = 110.478	β = 97.94
c = 37.777	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-12-26 
Deposition Author(s): Minasov, G., Shuvalova, L., Wawrzak, Z., Kiryukhina, O., Dubrovska, I., Anderson, W.F., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• 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