7BY3

Toxin-antitoxin complex from klebsiella pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb7BY3/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-04-21 Released: 2021-04-28 
• Deposition Author(s): Kang, S.M.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.279 
• R-Value Work: 0.244 

Literature

Toxin-antitoxin complex from klebsiella pneumoniae

Kang, S.M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 48.48 kDa 
• Atom Count: 3,189 
• Modelled Residue Count: 372 
• Deposited Residue Count: 418 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CopG family transcriptional regulator	A, C	82	Klebsiella pneumoniae	Mutation(s): 0  Gene Names:  yiiF, B4U21_30180, B4U25_36990, B4U61_14815, B6R99_17700, BANRA_02143, BANRA_02521, BANRA_02705, BL124_00012815, BN49_4676, C2U49_19540, C3F39_14645, C4Y50_020990, C7V41_25295, CK508_014375, DD581_07355, DD583_18720, DM059_31040, DM060_29565, DM062_35665, DM078_20205, EAO17_14145, EXT45_23360, F0330_15215, F1D54_19805, F3G17_14565, F3G25_25430, FAM29_17470, FAT93_13335, FCH06_017260, FXN60_10800, FXN67_21280, FZ928_20910, FZ929_16080, NCTC11679_05637, NCTC13443_00678, NCTC13635_03530, NCTC204_01866, NCTC8849_00074, NCTC9128_03825, NCTC9140_00751, NCTC9617_03579, NCTC9637_06504, SAMEA104567806_05449, SAMEA104567903_04890, SAMEA1712987_04768, SAMEA24002668_04178, SAMEA3531867_04820, SAMEA3649709_04060, SAMEA3673128_04237, SAMEA4364603_04577, SAMEA4873575_05060, SK89_02101
UniProt
Find proteins for W9BQC4 (Klebsiella pneumoniae) Explore W9BQC4  Go to UniProtKB:  W9BQC4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease VapC	B, D	127	Klebsiella pneumoniae	Mutation(s): 0  Gene Names:  vapC, B4U21_30185, B4U61_14820, B6R99_17695, BANRA_02522, BL124_00012810, BN49_4675, C1459_03020, C2U49_19545, C3F39_14640, C4Y50_020995, C7V41_25300, CK508_014380, DD581_07360, DM060_29570, DM078_20200, EAO17_14150, F1D54_19800, F3G25_25425, FAT93_13340, FCH06_017265, FXN60_10805, NCTC11679_05636, NCTC13443_00679, NCTC13465_05507, NCTC1936_00156, NCTC204_01865, NCTC8849_00075, NCTC9128_03826, SAMEA104567806_05448, SAMEA1712987_04767, SAMEA24002668_04177, SAMEA3531867_04819, SAMEA3649709_04059, SAMEA3673128_04238, SK89_02102 EC: 3.1
UniProt
Find proteins for A0A447RTX7 (Klebsiella pneumoniae) Explore A0A447RTX7  Go to UniProtKB:  A0A447RTX7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.279 
• R-Value Work: 0.244 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.435	α = 90
b = 79.019	β = 89.98
c = 59.609	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-04-28 
Deposition Author(s): Kang, S.M.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)		--

Revision History  

• Version 1.0: 2021-04-28
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references