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- PDB-5jf0: 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: 5jf0 | ||||||
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Title | Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with tripeptide Met-Ala-Arg | ||||||
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![]() | HYDROLASE / PDF / type 2 / NME / N-terminal methionine excision / Streptococcus agalactiae / inhibitor / tripeptide | ||||||
Function / homology | ![]() peptide deformylase / peptide deformylase activity / translation / metal ion binding 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 | ![]() | 104.3 KB | Display | ![]() |
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PDB format | ![]() | 78 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.6 KB | Display | ![]() |
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Full document | ![]() | 437.3 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 21.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jexC ![]() 5jeyC ![]() 5jezC ![]() 5jf1C ![]() 5jf2C ![]() 5jf3C ![]() 5jf4C ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 22910.297 Da / Num. of mol.: 1 / Mutation: S2A Source method: isolated from a genetically manipulated source Details: Methionine 16 is oxidized. / Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Protein/peptide | Mass: 377.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() | ||
#3: Chemical | ChemComp-ACT / | ||
#4: Chemical | ChemComp-NI / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 6% PEG-8000, 100mM Na Cacodylate pH6.5, 300mM Zn acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 31676 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.02 % / Rsym value: 0.059 / Net I/σ(I): 20.07 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 6.14 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 5.4 / % possible all: 96.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2AIE Resolution: 1.6→44.28 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.392 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.083 / 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: 17.54 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→44.28 Å
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Refine LS restraints |
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