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Yorodumi- PDB-3u7l: Crystal structures of the Staphylococcus aureus peptide deformyla... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3u7l | ||||||
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Title | Crystal structures of the Staphylococcus aureus peptide deformylase in complex with two classes of new inhibitors | ||||||
Components | Peptide deformylase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / PDF-INHIBITOR / PDF / PEPTIDE DEFORMYLASE / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information peptide deformylase / peptide deformylase activity / translation / metal ion binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Lee, S.J. / Lee, S.-J. / Lee, S.K. / Yoon, H.-J. / Lee, H.H. / Kim, K.K. / Lee, B.J. / Suh, S.W. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Structures of Staphylococcus aureus peptide deformylase in complex with two classes of new inhibitors Authors: Lee, S.J. / Lee, S.-J. / Lee, S.K. / Yoon, H.-J. / Lee, H.H. / Kim, K.K. / Lee, B.J. / Lee, B.I. / Suh, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u7l.cif.gz | 54.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u7l.ent.gz | 38.1 KB | Display | PDB format |
PDBx/mmJSON format | 3u7l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u7/3u7l ftp://data.pdbj.org/pub/pdb/validation_reports/u7/3u7l | HTTPS FTP |
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-Related structure data
Related structure data | 3u7kC 3u7mC 3u7nC 1q1yS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 21692.713 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: COL / Gene: sacol1100 / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q5HGZ3, peptide deformylase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-UDB / ( |
#4: 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: 3.14 Å3/Da / Density % sol: 60.79 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 23%(w/v) PEG 4000, 50mM Tris-HCl, 15%(v/v) glycerol, 100mM MgCl2, 20mM CaCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9722 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 26, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9722 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 18445 / % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Q1Y Resolution: 2.01→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.541 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R Free: 0.147 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.101 Å2
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Refinement step | Cycle: LAST / Resolution: 2.01→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.011→2.063 Å / Total num. of bins used: 20
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