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Yorodumi- PDB-7az8: DNA polymerase sliding clamp from Escherichia coli with peptide 4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7az8 | ||||||||||||
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Title | DNA polymerase sliding clamp from Escherichia coli with peptide 43 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: 1.61 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 | 7az8.cif.gz | 193.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7az8.ent.gz | 148.7 KB | Display | PDB format |
PDBx/mmJSON format | 7az8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/7az8 ftp://data.pdbj.org/pub/pdb/validation_reports/az/7az8 | HTTPS FTP |
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-Related structure data
Related structure data | 7az5C 7az6C 7az7C 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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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 4 molecules ABHI
#1: Protein | Mass: 42801.863 Da / Num. of mol.: 2 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: 868.028 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 4 types, 1015 molecules
#3: Chemical | ChemComp-PEG / #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Details
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: 2.66 Å3/Da / Density % sol: 53.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / Details: 0.2 M DL Malic acid pH 7, 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: 1.61→54.74 Å / Num. obs: 87336 / % possible obs: 88.2 % / Redundancy: 6.8 % / Biso Wilson estimate: 25.43 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.036 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.61→1.63 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 68 / CC1/2: 0.26 / Rpim(I) all: 1.187 |
-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: 1.61→54.74 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU R Cruickshank DPI: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.117 / SU Rfree Blow DPI: 0.107 / SU Rfree Cruickshank DPI: 0.103
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Displacement parameters | Biso max: 108.87 Å2 / Biso mean: 29.29 Å2 / Biso min: 10.57 Å2
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Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.61→54.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.61→1.71 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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