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Yorodumi- PDB-7etr: Crystal structure of SO_1444-SO_1445 complex from Shewanella onei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7etr | ||||||
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Title | Crystal structure of SO_1444-SO_1445 complex from Shewanella oneidensis | ||||||
Components |
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Keywords | TOXIN / toxin-antitoxin / ParE toxin / neutralization mechanism | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Shewanella oneidensis MR-1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.804 Å | ||||||
Authors | Zhou, J. / Zhang, H. | ||||||
Funding support | China, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7etr.cif.gz | 139.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7etr.ent.gz | 117.4 KB | Display | PDB format |
PDBx/mmJSON format | 7etr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/7etr ftp://data.pdbj.org/pub/pdb/validation_reports/et/7etr | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 | 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 interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350 and 0.2 M tri-sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9788 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 26, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 310.63 Å2 / Biso mean: 138.358 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.804→33.93 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 88.5833 Å / Origin y: 53.4863 Å / Origin z: 18.3364 Å
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Refinement TLS group |
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