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Yorodumi- PDB-7azl: DNA polymerase sliding clamp from Escherichia coli with peptide 3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7azl | |||||||||
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Title | DNA polymerase sliding clamp from Escherichia coli with peptide 38 bound | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN / antibacterial drug | |||||||||
Function / homology | DI(HYDROXYETHYL)ETHER / : Function and homology information | |||||||||
Biological species | Escherichia coli 2-427-07_S4_C3 (bacteria) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å | |||||||||
Authors | Monsarrat, C. / Compain, G. / Andre, C. / Martiel, I. / Engilberge, S. / Olieric, V. / Wolff, P. / Brillet, K. / Landolfo, M. / Silva da Veiga, C. ...Monsarrat, C. / Compain, G. / Andre, C. / Martiel, I. / Engilberge, S. / Olieric, V. / Wolff, P. / Brillet, K. / Landolfo, M. / Silva da Veiga, C. / Wagner, J. / Guichard, G. / Burnouf, D.Y. | |||||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Iterative Structure-Based Optimization of Short Peptides Targeting the Bacterial Sliding Clamp. Authors: Monsarrat, C. / Compain, G. / Andre, C. / Engilberge, S. / Martiel, I. / Olieric, V. / Wolff, P. / Brillet, K. / Landolfo, M. / Silva da Veiga, C. / Wagner, J. / Guichard, G. / Burnouf, D.Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7azl.cif.gz | 306.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7azl.ent.gz | 243.8 KB | Display | PDB format |
PDBx/mmJSON format | 7azl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/7azl ftp://data.pdbj.org/pub/pdb/validation_reports/az/7azl | HTTPS FTP |
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-Related structure data
Related structure data | 7az5C 7az6C 7az7C 7az8C 7azcC 7azdC 7azeC 7azfC 7azgC 7azkC 6fvlS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: Protein | Mass: 42801.863 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli 2-427-07_S4_C3 (bacteria) Gene: dnaN, AD31_4438 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A073FMV0 #2: Protein/peptide | Mass: 890.849 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-GOL / | #4: Chemical | #5: Water | ChemComp-HOH / | 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: 2.72 Å3/Da / Density % sol: 54.71 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / Details: 0.2 M Sodium formate pH 7.2, PEG 3350 20% (w/v) |
-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 / Detector: PIXEL / Date: Nov 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.42→70.69 Å / Num. obs: 70023 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.99 / Rpim(I) all: 0.051 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.42→2.46 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3408 / CC1/2: 0.72 / Rpim(I) all: 0.39 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FVL Resolution: 2.42→70.69 Å / Cross valid method: THROUGHOUT Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 49.63 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.42→70.69 Å
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Refine LS restraints |
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