6NBG

2.05 Angstrom Resolution Crystal Structure of Hypothetical Protein KP1_5497 from Klebsiella pneumoniae.

• PDB DOI: https://doi.org/10.2210/pdb6NBG/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-12-07 Released: 2018-12-19 
• Deposition Author(s): Minasov, G., Shuvalova, L., Kiryukhina, O., Dubrovska, I., 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: 2.05 Å
• R-Value Free: 0.231 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 

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: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 161.28 kDa 
• Atom Count: 11,887 
• Modelled Residue Count: 1,442 
• Deposited Residue Count: 1,452 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosamine-6-phosphate deaminase	A, B, C, D, E, F	242	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: nagB_2, DM059_30720, SAMEA4364603_04465 EC: 3.5.99.6
UniProt
Find proteins for A0A332QZQ2 (Klebsiella pneumoniae) Explore A0A332QZQ2  Go to UniProtKB:  A0A332QZQ2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	G [auth A], H [auth B], J [auth D], K [auth D], L [auth E], M [auth E], N [auth F], O [auth F]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	I [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.231 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 
• Space Group: C 2 2 2₁
• Diffraction Data: https://doi.org/10.18430/m36nbg

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.482	α = 90
b = 123.806	β = 90
c = 299.664	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-12-19 
Deposition Author(s): Minasov, G., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2018-12-19
  Type: Initial release
  
• Version 1.1: 2023-06-14
  Changes: Database references, Refinement description
• Version 1.2: 2024-10-09
  Changes: Data collection, Structure summary