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Yorodumi- PDB-7ocj: Crystal structure of E.coli LexA in complex with nanobody NbSOS2(... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ocj | ||||||
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Title | Crystal structure of E.coli LexA in complex with nanobody NbSOS2(Nb14509) | ||||||
Components |
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Keywords | TRANSCRIPTION / Transcriptional repressor DNA binding autoproteolysis Nanobodies | ||||||
Function / homology | Function and homology information repressor LexA / SOS response / DNA replication / serine-type endopeptidase activity / DNA repair / negative regulation of DNA-templated transcription / proteolysis / DNA binding Similarity search - Function | ||||||
Biological species | Lama glama (llama) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Maso, L. / Vascon, F. / Chinellato, M. / Pardon, E. / Steyaert, J. / Angelini, A. / Tondi, D. / Cendron, L. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Structure / Year: 2022 Title: Nanobodies targeting LexA autocleavage disclose a novel suppression strategy of SOS-response pathway. Authors: Maso, L. / Vascon, F. / Chinellato, M. / Goormaghtigh, F. / Bellio, P. / Campagnaro, E. / Van Melderen, L. / Ruzzene, M. / Pardon, E. / Angelini, A. / Celenza, G. / Steyaert, J. / Tondi, D. / Cendron, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ocj.cif.gz | 376.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ocj.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7ocj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/7ocj ftp://data.pdbj.org/pub/pdb/validation_reports/oc/7ocj | HTTPS FTP |
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-Related structure data
Related structure data | 7b5gC 7zraC 1jhfS 7bg2 C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 12422.886 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) #2: Protein | Mass: 24560.086 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: missing residues are not visible in the electron density maps Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lexA, EAMG_02325 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X3HXW2, repressor LexA #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.47 Å3/Da / Density % sol: 50.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M lithium sulfate, 0.1 M sodium acetate pH 4.5, 30 % w/v PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.96546 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 14, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96546 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→48.79 Å / Num. obs: 28568 / % possible obs: 96.2 % / Redundancy: 7.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.126 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.7→2.83 Å / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 8056 / CC1/2: 0.558 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JHF Resolution: 2.7→48.25 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 93.72 Å2 / Biso mean: 47.6129 Å2 / Biso min: 30 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→48.25 Å
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