7BY3 | pdb_00007by3

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.279 (Depositor), 0.268 (DCC)
R-Value Work:
0.244 (Depositor), 0.243 (DCC)

wwPDB Validation 3D Report Full Report

Validation slider image for 7BY3

This is version 1.1 of the entry. See complete history.

Literature

Toxin-antitoxin complex from klebsiella pneumoniae

Kang, S.M.

To be published.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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... 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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	W9BQC4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

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... 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A447RTX7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.279 (Depositor), 0.268 (DCC)
R-Value Work: 0.244 (Depositor), 0.243 (DCC)

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

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-04-28

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.