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Yorodumi- PDB-5jf7: Crystal structure of type 2 PDF from Streptococcus agalactiae in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jf7 | ||||||
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Title | Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with inhibitor SMP289 | ||||||
Components | Peptide deformylase | ||||||
Keywords | HYDROLASE / PDF / type 2 / NME / N-terminal methionine excision / Streptococcus agalactiae / inhibitor / SMP289 | ||||||
Function / homology | Function and homology information peptide deformylase / peptide deformylase activity / translation / metal ion binding Similarity search - Function | ||||||
Biological species | Streptococcus agalactiae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Fieulaine, S. / Giglione, C. / Meinnel, T. / Hamiche, K. | ||||||
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 | 5jf7.cif.gz | 100.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jf7.ent.gz | 75 KB | Display | PDB format |
PDBx/mmJSON format | 5jf7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/5jf7 ftp://data.pdbj.org/pub/pdb/validation_reports/jf/5jf7 | HTTPS FTP |
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-Related structure data
Related structure data | 5jexC 5jeyC 5jezC 5jf0C 5jf1C 5jf2C 5jf3C 5jf4C 5jf5C 5jf6C 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
-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.) Streptococcus agalactiae (bacteria) / Gene: def, gbs1883 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2,pLysS / References: UniProt: Q8E378, peptide deformylase |
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-Non-polymers , 5 types, 245 molecules
#2: Chemical | ChemComp-6JU / | ||
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 13% PEG-8000, 100mM Imidazole pH6.5, 400mM Zn acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 28, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→50 Å / Num. obs: 26386 / % possible obs: 94.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rsym value: 0.093 / Net I/σ(I): 12.04 |
Reflection shell | Resolution: 2.09→2.22 Å / Redundancy: 3.16 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 3.99 / Rsym value: 0.381 / % possible all: 86.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AIE Resolution: 2.1→44.66 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.174 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.14 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→44.66 Å
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Refine LS restraints |
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