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- PDB-4ml0: Crystal structure of E.coli DinJ-YafQ complex -

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Basic information

Entry
Database: PDB / ID: 4ml0
TitleCrystal structure of E.coli DinJ-YafQ complex
Components
  • Predicted antitoxin of YafQ-DinJ toxin-antitoxin system
  • Predicted toxin of the YafQ-DinJ toxin-antitoxin system
KeywordsTOXIN/ANTITOXIN / RHH motif / interferase / TOXIN-ANTITOXIN complex
Function / homology
Function and homology information


cis-regulatory region sequence-specific DNA binding => GO:0000987 / single-species biofilm formation / toxic substance binding / endonuclease activity / Hydrolases; Acting on ester bonds / regulation of DNA-templated transcription / DNA binding / RNA binding
Similarity search - Function
Antitoxin DinJ / RelB antitoxin/Antitoxin DinJ / RelB antitoxin / Toxin-antitoxin system, YafQ-like toxin / Bacterial toxin of type II toxin-antitoxin system, YafQ / RelE-like / Toxin-antitoxin system, RelE/ParE toxin family / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / Arc-type ribbon-helix-helix ...Antitoxin DinJ / RelB antitoxin/Antitoxin DinJ / RelB antitoxin / Toxin-antitoxin system, YafQ-like toxin / Bacterial toxin of type II toxin-antitoxin system, YafQ / RelE-like / Toxin-antitoxin system, RelE/ParE toxin family / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / Arc-type ribbon-helix-helix / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
mRNA interferase toxin YafQ / Antitoxin DinJ / : / :
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsLiang, Y.J. / Gao, Z.Q. / Liu, Q.S. / Dong, Y.H.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural and Functional Characterization of Escherichia coli Toxin-Antitoxin Complex DinJ-YafQ
Authors: Liang, Y. / Gao, Z. / Wang, F. / Zhang, Y. / Dong, Y. / Liu, Q.
History
DepositionSep 6, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Predicted antitoxin of YafQ-DinJ toxin-antitoxin system
B: Predicted toxin of the YafQ-DinJ toxin-antitoxin system
C: Predicted antitoxin of YafQ-DinJ toxin-antitoxin system
D: Predicted toxin of the YafQ-DinJ toxin-antitoxin system
E: Predicted antitoxin of YafQ-DinJ toxin-antitoxin system
F: Predicted toxin of the YafQ-DinJ toxin-antitoxin system
G: Predicted antitoxin of YafQ-DinJ toxin-antitoxin system
H: Predicted toxin of the YafQ-DinJ toxin-antitoxin system
I: Predicted antitoxin of YafQ-DinJ toxin-antitoxin system
J: Predicted toxin of the YafQ-DinJ toxin-antitoxin system
K: Predicted antitoxin of YafQ-DinJ toxin-antitoxin system
L: Predicted toxin of the YafQ-DinJ toxin-antitoxin system
M: Predicted antitoxin of YafQ-DinJ toxin-antitoxin system
N: Predicted toxin of the YafQ-DinJ toxin-antitoxin system
O: Predicted antitoxin of YafQ-DinJ toxin-antitoxin system
P: Predicted toxin of the YafQ-DinJ toxin-antitoxin system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,23458
Polymers166,19916
Non-polymers4,03542
Water22,0321223
1
A: Predicted antitoxin of YafQ-DinJ toxin-antitoxin system
B: Predicted toxin of the YafQ-DinJ toxin-antitoxin system
C: Predicted antitoxin of YafQ-DinJ toxin-antitoxin system
D: Predicted toxin of the YafQ-DinJ toxin-antitoxin system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,51014
Polymers41,5504
Non-polymers96110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13210 Å2
ΔGint-231 kcal/mol
Surface area16900 Å2
MethodPISA
2
E: Predicted antitoxin of YafQ-DinJ toxin-antitoxin system
F: Predicted toxin of the YafQ-DinJ toxin-antitoxin system
G: Predicted antitoxin of YafQ-DinJ toxin-antitoxin system
H: Predicted toxin of the YafQ-DinJ toxin-antitoxin system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,51014
Polymers41,5504
Non-polymers96110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12940 Å2
ΔGint-204 kcal/mol
Surface area17080 Å2
MethodPISA
3
I: Predicted antitoxin of YafQ-DinJ toxin-antitoxin system
J: Predicted toxin of the YafQ-DinJ toxin-antitoxin system
K: Predicted antitoxin of YafQ-DinJ toxin-antitoxin system
L: Predicted toxin of the YafQ-DinJ toxin-antitoxin system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,60615
Polymers41,5504
Non-polymers1,05711
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13000 Å2
ΔGint-208 kcal/mol
Surface area17010 Å2
MethodPISA
4
M: Predicted antitoxin of YafQ-DinJ toxin-antitoxin system
N: Predicted toxin of the YafQ-DinJ toxin-antitoxin system
O: Predicted antitoxin of YafQ-DinJ toxin-antitoxin system
P: Predicted toxin of the YafQ-DinJ toxin-antitoxin system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,60615
Polymers41,5504
Non-polymers1,05711
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13820 Å2
ΔGint-253 kcal/mol
Surface area17020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.901, 120.250, 120.201
Angle α, β, γ (deg.)90.00, 130.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Predicted antitoxin of YafQ-DinJ toxin-antitoxin system


Mass: 9649.993 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: B / REL606 / Gene: dinJ, ECB_00221 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C6UAV3, UniProt: A0A140ND86*PLUS
#2: Protein
Predicted toxin of the YafQ-DinJ toxin-antitoxin system


Mass: 11124.896 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: B / REL606 / Gene: yafQ, ECB_00220 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C6UAV2, UniProt: A0A140NAP5*PLUS
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1223 / Source method: isolated from a natural source / Formula: H2O

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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: 2.91 Å3/Da / Density % sol: 57.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2M (NH4)2SO4, 2.5% 2-Propanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 3, 2012
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 111791 / Num. obs: 110921 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 33
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 9.32 / Num. unique all: 5575 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→43.713 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2151 5539 5 %random
Rwork0.1748 ---
all0.1768 110921 --
obs0.1748 110779 99.89 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.501 Å2 / ksol: 0.359 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.2773 Å2-0 Å2-1.4656 Å2
2---1.2153 Å2-0 Å2
3----2.062 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.713 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11132 0 210 1223 12565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811510
X-RAY DIFFRACTIONf_angle_d1.06315543
X-RAY DIFFRACTIONf_dihedral_angle_d13.774319
X-RAY DIFFRACTIONf_chiral_restr0.0721733
X-RAY DIFFRACTIONf_plane_restr0.0041950
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.12390.24432070.1923485100
2.1239-2.14890.25191660.17753524100
2.1489-2.17510.23531850.17733475100
2.1751-2.20260.22951800.17493510100
2.2026-2.23160.23711810.17633511100
2.2316-2.26210.25251780.1773482100
2.2621-2.29450.26052000.17833499100
2.2945-2.32870.23681900.18483489100
2.3287-2.36510.25111990.17313496100
2.3651-2.40390.22961950.18493493100
2.4039-2.44530.25272020.18783473100
2.4453-2.48980.25181840.18093497100
2.4898-2.53760.21731900.18033516100
2.5376-2.58940.24031770.18183466100
2.5894-2.64570.25321840.18713496100
2.6457-2.70730.22651930.19273498100
2.7073-2.7750.24261710.18823536100
2.775-2.850.20621830.18243512100
2.85-2.93380.24251820.18553511100
2.9338-3.02850.22941850.18783501100
3.0285-3.13670.23821690.18653552100
3.1367-3.26230.22231850.18013508100
3.2623-3.41070.19081750.17413516100
3.4107-3.59040.21151790.16613510100
3.5904-3.81530.2021760.15953542100
3.8153-4.10960.17911950.15713496100
4.1096-4.52280.16861680.14583542100
4.5228-5.17640.17821630.14893570100
5.1764-6.51820.2042000.19383538100
6.5182-43.72230.18231970.1851349697

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