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- PDB-7by3: Toxin-antitoxin complex from klebsiella pneumoniae -

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Basic information

Entry
Database: PDB / ID: 7by3
TitleToxin-antitoxin complex from klebsiella pneumoniae
Components
  • CopG family transcriptional regulator
  • Ribonuclease VapC
KeywordsHYDROLASE / protein complex
Function / homology
Function and homology information


RNA nuclease activity / toxin activity / sequence-specific DNA binding / Hydrolases; Acting on ester bonds / regulation of DNA-templated transcription / magnesium ion binding
Similarity search - Function
Predicted DNA-binding protein, ribbon-helix-helix domain / Ribbon-helix-helix domain / PIN domain / VapC family / Arc-type ribbon-helix-helix / PIN domain / PIN-like domain superfamily
Similarity search - Domain/homology
Ribonuclease VapC / CopG family transcriptional regulator
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKang, S.M.
Funding support1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)
CitationJournal: To Be Published
Title: Toxin-antitoxin complex from klebsiella pneumoniae
Authors: Kang, S.M.
History
DepositionApr 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CopG family transcriptional regulator
B: Ribonuclease VapC
C: CopG family transcriptional regulator
D: Ribonuclease VapC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4835
Polymers48,3874
Non-polymers961
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8640 Å2
ΔGint-72 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.435, 79.019, 59.609
Angle α, β, γ (deg.)90.000, 89.980, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein CopG family transcriptional regulator / Putative CopG-family DNA-binding protein / Ribbon-helix-helix domain-containing protein / YiiF protein


Mass: 9799.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: 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, ...Gene: 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
Production host: Escherichia coli (E. coli) / References: UniProt: W9BQC4
#2: Protein Ribonuclease VapC / RNase VapC / Toxin VapC


Mass: 14394.575 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: 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, ...Gene: 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
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0W8AM92, Hydrolases; Acting on ester bonds
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Tris

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 31667 / % possible obs: 96.8 % / Redundancy: 4.4 % / Rpim(I) all: 0.037 / Net I/σ(I): 48.3
Reflection shellResolution: 2.04→2.08 Å / Num. unique obs: 1644 / Rpim(I) all: 0.267

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Processing

Software
NameVersionClassification
PHENIX1.18refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.27923 1618 -
Rwork0.2443 --
obs-31665 96.63 %
Displacement parametersBiso mean: 45.88 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3010 0 5 177 3192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00593060
X-RAY DIFFRACTIONf_angle_d1.22044133
X-RAY DIFFRACTIONf_chiral_restr0.0545465
X-RAY DIFFRACTIONf_plane_restr0.0043534
X-RAY DIFFRACTIONf_dihedral_angle_d17.40391889
LS refinement shellResolution: 2.04→2.08 Å /
Num. reflection% reflection
obs1644 99.9 %

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