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- PDB-7aze: DNA polymerase sliding clamp from Escherichia coli with peptide 1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7aze | |||||||||
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Title | DNA polymerase sliding clamp from Escherichia coli with peptide 18 bound | |||||||||
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![]() | DNA BINDING PROTEIN / antibacterial drug | |||||||||
Function / homology | MALONATE ION / : ![]() | |||||||||
Biological species | ![]() ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | 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. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 319.7 KB | Display | ![]() |
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PDB format | ![]() | 255.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 482.5 KB | Display | ![]() |
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Full document | ![]() | 484.7 KB | Display | |
Data in XML | ![]() | 35.9 KB | Display | |
Data in CIF | ![]() | 54.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7az5C ![]() 7az6C ![]() 7az7C ![]() 7az8C ![]() 7azcC ![]() 7azdC ![]() 7azfC ![]() 7azgC ![]() 7azkC ![]() 7azlC ![]() 6fvlS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() Gene: dnaN, AD31_4438 / Production host: ![]() ![]() #2: Protein/peptide | Mass: 822.919 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 4 types, 746 molecules ![](data/chem/img/MLI.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MLI / | ||||
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#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / Details: 8% v/v Tacsimate pH 6.0, PEG 3350 20% (w/v) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.82→53.86 Å / Num. obs: 60806 / % possible obs: 90.3 % / Redundancy: 6 % / Biso Wilson estimate: 24.07 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.091 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.82→1.99 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3041 / CC1/2: 0.844 / Rpim(I) all: 1.154 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6FVL Resolution: 1.82→52.87 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.182 / SU Rfree Blow DPI: 0.157 / SU Rfree Cruickshank DPI: 0.153
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Displacement parameters | Biso max: 104.9 Å2 / Biso mean: 28.95 Å2 / Biso min: 5.55 Å2
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Refine analyze | Luzzati coordinate error obs: 0.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.82→52.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.82→1.94 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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