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- PDB-7etr: Crystal structure of SO_1444-SO_1445 complex from Shewanella onei... -

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Basic information

Entry
Database: PDB / ID: 7etr
TitleCrystal structure of SO_1444-SO_1445 complex from Shewanella oneidensis
Components
  • Toxin module of toxin-antitoxin system RelE/StbE family
  • Transcriptional regulator CopG family
KeywordsTOXIN / toxin-antitoxin / ParE toxin / neutralization mechanism
Function / homology
Function and homology information


regulation of DNA-templated transcription
Similarity search - Function
: / ParE toxin of type II toxin-antitoxin system, parDE / Toxin-antitoxin system, RelE/ParE toxin family / Ribbon-helix-helix protein, CopG / Ribbon-helix-helix protein, copG family / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / Arc-type ribbon-helix-helix / Ribbon-helix-helix
Similarity search - Domain/homology
Transcriptional regulator CopG family / Toxin module of toxin-antitoxin system RelE/StbE family
Similarity search - Component
Biological speciesShewanella oneidensis MR-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.804 Å
AuthorsZhou, J. / Zhang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U1732113, 31670059 China
CitationJournal: Microorganisms / Year: 2021
Title: Insights into the Neutralization and DNA Binding of Toxin-Antitoxin System ParE SO-CopA SO by Structure-Function Studies.
Authors: Zhou, J. / Du, X.J. / Liu, Y. / Gao, Z.Q. / Geng, Z. / Dong, Y.H. / Zhang, H.
History
DepositionMay 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator CopG family
B: Transcriptional regulator CopG family
C: Toxin module of toxin-antitoxin system RelE/StbE family
D: Toxin module of toxin-antitoxin system RelE/StbE family


Theoretical massNumber of molelcules
Total (without water)46,4294
Polymers46,4294
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7390 Å2
ΔGint-47 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.404, 85.404, 110.918
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Transcriptional regulator CopG family / Antitoxin SO_1445


Mass: 11980.932 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis MR-1 (bacteria) / Strain: MR-1 / Gene: SO_1445 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EGZ2
#2: Protein Toxin module of toxin-antitoxin system RelE/StbE family / Toxin SO_1444


Mass: 11233.428 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis MR-1 (bacteria) / Strain: MR-1 / Gene: SO_1444 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EGZ3
Has ligand of interestY
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350 and 0.2 M tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9788 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 7720 / % possible obs: 100 % / Redundancy: 20 % / Biso Wilson estimate: 133 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.048 / Rrim(I) all: 0.205 / Net I/σ(I): 52
Reflection shellResolution: 3.8→3.87 Å / Rmerge(I) obs: 0.796 / Mean I/σ(I) obs: 7.2 / Num. unique obs: 375 / CC1/2: 0.995 / Rpim(I) all: 0.155 / Rrim(I) all: 0.752 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 3.804→33.93 Å / SU ML: 0.65 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 38.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3078 770 10.04 %
Rwork0.2875 6897 -
obs0.2895 7667 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 310.63 Å2 / Biso mean: 138.358 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.804→33.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2582 0 0 0 2582
Num. residues----315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052663
X-RAY DIFFRACTIONf_angle_d0.8063583
X-RAY DIFFRACTIONf_chiral_restr0.041393
X-RAY DIFFRACTIONf_plane_restr0.006458
X-RAY DIFFRACTIONf_dihedral_angle_d18.971624
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.8041-4.04210.40431240.35291147100
4.0421-4.35360.36461320.29611148100
4.3536-4.79060.3071320.31561158100
4.7906-5.48130.37991230.31591144100
5.4813-6.89640.34081270.32641158100
6.8964-33.90.24431320.2361114299
Refinement TLS params.Method: refined / Origin x: 88.5833 Å / Origin y: 53.4863 Å / Origin z: 18.3364 Å
111213212223313233
T0.6654 Å20.1382 Å2-0.1003 Å2-0.8639 Å20.0373 Å2--0.7218 Å2
L0.5096 °2-1.1746 °20.7788 °2-0.5533 °21.0904 °2---0.0986 °2
S0.2598 Å °-0.0226 Å °-0.2606 Å °0.0139 Å °0.0412 Å °0.3947 Å °0.1652 Å °-0.0493 Å °0.077 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA6 - 93
2X-RAY DIFFRACTION1allB5 - 77
3X-RAY DIFFRACTION1allC2 - 93
4X-RAY DIFFRACTION1allD2 - 93

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