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Yorodumi- PDB-8pat: Structure of the E.coli DNA polymerase sliding clamp with a coval... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pat | |||||||||
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Title | Structure of the E.coli DNA polymerase sliding clamp with a covalently bound peptide 3. | |||||||||
Components |
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Keywords | REPLICATION / sliding clamp / covalent peptide / antibiotics | |||||||||
Function / homology | Function and homology information DNA polymerase III complex / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase activity / DNA binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | |||||||||
Authors | Compain, G. / Monsarrat, C. / Blagojevic, J. / Brillet, K. / Dumas, P. / Hammann, P. / Kuhn, L. / Martiel, I. / Engilberge, S. / Olieric, V. ...Compain, G. / Monsarrat, C. / Blagojevic, J. / Brillet, K. / Dumas, P. / Hammann, P. / Kuhn, L. / Martiel, I. / Engilberge, S. / Olieric, V. / Wolff, P. / Burnouf, D. / Guichard, G. | |||||||||
Funding support | France, 2items
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Citation | Journal: Jacs Au / Year: 2024 Title: Peptide-Based Covalent Inhibitors Bearing Mild Electrophiles to Target a Conserved His Residue of the Bacterial Sliding Clamp. Authors: Compain, G. / Monsarrat, C. / Blagojevic, J. / Brillet, K. / Dumas, P. / Hammann, P. / Kuhn, L. / Martiel, I. / Engilberge, S. / Olieric, V. / Wolff, P. / Burnouf, D.Y. / Wagner, J. / Guichard, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pat.cif.gz | 179.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pat.ent.gz | 140.4 KB | Display | PDB format |
PDBx/mmJSON format | 8pat.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pa/8pat ftp://data.pdbj.org/pub/pdb/validation_reports/pa/8pat | HTTPS FTP |
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-Related structure data
Related structure data | 8payC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Experimental dataset #1 | Data reference: 10.2210/pdb6FVL/pdb / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40949.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dnaN / Production host: Escherichia coli (E. coli) / References: UniProt: C3SLM2 |
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#2: Protein/peptide | Mass: 727.891 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.42 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / Details: 0.2 M Potassium nitrate 20% PEG 3350, pH 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 2, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→54.81 Å / Num. obs: 79966 / % possible obs: 91.5 % / Observed criterion σ(I): 1.3 / Redundancy: 6.8 % / CC1/2: 0.99 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.37→1.45 Å / Num. unique obs: 3999 / CC1/2: 0.49 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→54.81 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→54.81 Å
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Refine LS restraints |
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LS refinement shell |
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