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- PDB-5jf4: Crystal structure of type 2 PDF from Streptococcus agalactiae in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jf4 | ||||||
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Title | Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with inhibitor AT019 | ||||||
![]() | Peptide deformylase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fieulaine, S. / Giglione, C. / Meinnel, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A unique peptide deformylase platform to rationally design and challenge novel active compounds. Authors: Fieulaine, S. / Alves de Sousa, R. / Maigre, L. / Hamiche, K. / Alimi, M. / Bolla, J.M. / Taleb, A. / Denis, A. / Pages, J.M. / Artaud, I. / Meinnel, T. / Giglione, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.9 KB | Display | ![]() |
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PDB format | ![]() | 75.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5jexC ![]() 5jeyC ![]() 5jezC ![]() 5jf0C ![]() 5jf1C ![]() 5jf2C ![]() 5jf3C ![]() 5jf5C ![]() 5jf6C ![]() 5jf7C ![]() 5jf8C ![]() 2aieS 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 , 1 types, 1 molecules A
#1: Protein | ![]() Mass: 22894.297 Da / Num. of mol.: 1 / Mutation: S2A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 205 molecules ![](data/chem/img/6JT.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-6JT / ( | ||
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#3: Chemical | ChemComp-ACT / ![]() | ||
#4: Chemical | ChemComp-IMD / ![]() | ||
#5: Chemical | ChemComp-ZN / #6: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.95 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 7% PEG-8000, 100mM imidazole pH7.5, 400mM Zn acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.4→50 Å / Num. obs: 18118 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.49 % / CC1/2: 0.987 / Rsym value: 0.183 / Net I/σ(I): 8.88 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 5.09 % / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 3.15 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2AIE Resolution: 2.4→44.28 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.804 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.363 / ESU R Free: 0.241 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.215 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→44.28 Å
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Refine LS restraints |
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