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- PDB-3u7n: Crystal structures of the Staphylococcus aureus peptide deformyla... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3u7n | ||||||
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Title | Crystal structures of the Staphylococcus aureus peptide deformylase in complex with two classes of new inhibitors | ||||||
![]() | Peptide deformylase | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / PDF-INHIBITOR / PDF / PEPTIDE DEFORMYLASE / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() peptide deformylase / peptide deformylase activity / translation / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lee, S.J. / Lee, S.-J. / Lee, S.K. / Yoon, H.-J. / Lee, H.H. / Kim, K.K. / Lee, B.J. / Suh, S.W. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 53.9 KB | Display | ![]() |
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PDB format | ![]() | 37.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 747.5 KB | Display | ![]() |
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Full document | ![]() | 750.6 KB | Display | |
Data in XML | ![]() | 10.9 KB | Display | |
Data in CIF | ![]() | 14.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3u7kC ![]() 3u7lC ![]() 3u7mC ![]() 1q1yS C: citing same article ( S: Starting model for refinement |
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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: 21692.713 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-UHF / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.32 % |
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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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 2, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 12218 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1Q1Y Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.121 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R Free: 0.197 / 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: 33.41 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.296→2.355 Å / Total num. of bins used: 20
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