5ZGN | pdb_00005zgn

The crystal structure of KacTA-DNA complex

• PDB DOI: https://doi.org/10.2210/pdb5ZGN/pdb
• NAKB: 5ZGN

• Classification: TOXIN
• Organism(s): Klebsiella pneumoniae subsp. pneumoniae HS11286, synthetic construct
• Expression System: Escherichia coli-Thermus thermophilus shuttle vector pTRH1T
• Mutation(s): No 


• Deposited: 2018-03-09 Released: 2019-04-03 
• Deposition Author(s): Qian, H.L., Yao, Q.Q., Gan, J.H., Ou, H.Y.
• Funding Organization(s): Ministry of Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 
  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Literature

The crystal structure of KacTA-DNA complex

Qian, H.L., Yao, Q.Q., Gan, J.H., Ou, H.Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A4B2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 97.67 kDa 
• Atom Count: 6,033 
• Modeled Residue Count: 674 
• Deposited Residue Count: 760 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KacA	A, B, D, E	88	Klebsiella pneumoniae subsp. pneumoniae HS11286	Mutation(s): 0  Gene Names: KPHS_05880
UniProt
Find proteins for A0A0H3GLZ1 (Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)) Explore A0A0H3GLZ1  Go to UniProtKB:  A0A0H3GLZ1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
KacT	C, F	177	Klebsiella pneumoniae subsp. pneumoniae HS11286	Mutation(s): 0  Gene Names: KPHS_05890
UniProt
Find proteins for A0A0H3GMP0 (Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)) Explore A0A0H3GMP0  Go to UniProtKB:  A0A0H3GMP0

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (27-MER)	G	27	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (27-MER)	H	27	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	I [auth A], J [auth C], K [auth F]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free:  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.046	α = 93.83
b = 62.044	β = 93.99
c = 61.994	γ = 93.93

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-04-03 
Deposition Author(s): Qian, H.L., Yao, Q.Q., Gan, J.H., Ou, H.Y.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology	China	2015CB554202

Revision History  

• Version 1.0: 2019-04-03
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Database references, Structure summary