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Yorodumi- PDB-7az5: DNA polymerase sliding clamp from Escherichia coli with peptide 4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7az5 | ||||||
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Title | DNA polymerase sliding clamp from Escherichia coli with peptide 47 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 / molecular replacement / Resolution: 1.87 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 | 7az5.cif.gz | 606.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7az5.ent.gz | 501.2 KB | Display | PDB format |
PDBx/mmJSON format | 7az5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/7az5 ftp://data.pdbj.org/pub/pdb/validation_reports/az/7az5 | HTTPS FTP |
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-Related structure data
Related structure data | 7az6C 7az7C 7az8C 7azcC 7azdC 7azeC 7azfC 7azgC 7azkC 7azlC 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 (E. coli) / References: UniProt: A0A073FMV0 #2: Protein/peptide | Mass: 818.013 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | #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: 2.22 Å3/Da / Density % sol: 44.66 % |
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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: 1.87→65.24 Å / Num. obs: 90577 / % possible obs: 93.5 % / Redundancy: 7 % / Biso Wilson estimate: 26.52 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.135 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.87→2.03 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4529 / CC1/2: 0.56 / Rpim(I) all: 0.526 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FVL Resolution: 1.87→27.35 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.217 / SU Rfree Blow DPI: 0.165 / SU Rfree Cruickshank DPI: 0.165
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Displacement parameters | Biso max: 130.1 Å2 / Biso mean: 34.66 Å2 / Biso min: 3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.26 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.87→27.35 Å
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LS refinement shell | Resolution: 1.87→1.97 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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