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Yorodumi- PDB-5jf0: Crystal structure of type 2 PDF from Streptococcus agalactiae in ... -
+Open data
-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 | ||||||
Components |
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Keywords | HYDROLASE / PDF / type 2 / NME / N-terminal methionine excision / Streptococcus agalactiae / inhibitor / tripeptide | ||||||
Function / homology | Function and homology information peptide deformylase / peptide deformylase activity / translation / metal ion binding Similarity search - Function | ||||||
Biological species | Streptococcus agalactiae (bacteria) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Fieulaine, S. / Giglione, C. / Meinnel, T. | ||||||
Funding support | France, 1items
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Citation | Journal: Sci Rep / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jf0.cif.gz | 104.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jf0.ent.gz | 78 KB | Display | PDB format |
PDBx/mmJSON format | 5jf0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jf0_validation.pdf.gz | 436.6 KB | Display | wwPDB validaton report |
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Full document | 5jf0_full_validation.pdf.gz | 437.3 KB | Display | |
Data in XML | 5jf0_validation.xml.gz | 14 KB | Display | |
Data in CIF | 5jf0_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/5jf0 ftp://data.pdbj.org/pub/pdb/validation_reports/jf/5jf0 | 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 (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
#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.) Streptococcus agalactiae (bacteria) / Gene: def, gbs1883 / Plasmid: pET16b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 pLysS / References: UniProt: Q8E378, peptide deformylase | ||
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#2: Protein/peptide | Mass: 377.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) | ||
#3: Chemical | ChemComp-ACT / | ||
#4: Chemical | ChemComp-NI / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å |
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 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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