+Open data
-Basic information
Entry | Database: PDB / ID: 6ow7 | ||||||
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Title | X-ray Structure of Polypeptide Deformylase with a Piperazic Acid | ||||||
Components | Peptide deformylase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Inhibitor / complex / metal protein / enzyme / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information co-translational protein modification / peptide deformylase / peptide deformylase activity / translation / metal ion binding Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Campobasso, N. / Spletstoser, J. / Ward, P. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2019 Title: Discovery of piperazic acid peptide deformylase inhibitors with in vivo activity for respiratory tract and skin infections. Authors: Spletstoser, J.T. / Dreabit, J. / Knox, A.N. / Benowitz, A. / Campobasso, N. / Ward, P. / Cui, G. / Lewandowski, T. / McCloskey, L. / Aubart, K.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ow7.cif.gz | 116.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ow7.ent.gz | 73 KB | Display | PDB format |
PDBx/mmJSON format | 6ow7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/6ow7 ftp://data.pdbj.org/pub/pdb/validation_reports/ow/6ow7 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22589.854 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) Gene: defB, def, def_1, def_2, def_3, A5N45_09745, ERS019420_01538, ERS019688_00954, ERS020178_05158, ERS020534_01685, ERS020726_00048, ERS021057_00383, ERS021733_04069, ERS050646_01998, ERS367886_ ...Gene: defB, def, def_1, def_2, def_3, A5N45_09745, ERS019420_01538, ERS019688_00954, ERS020178_05158, ERS020534_01685, ERS020726_00048, ERS021057_00383, ERS021733_04069, ERS050646_01998, ERS367886_01588, ERS409327_03241, ERS409593_03947, KK0981_34260, NCTC12140_00964 Production host: Escherichia coli (E. coli) References: UniProt: Q939R9, UniProt: Q8DP79*PLUS, peptide deformylase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.69 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1 % - 4 % PEG400 45 % - 55% Ammonium Sulfate 0.1 M HEPES |
-Data collection
Diffraction | Mean temperature: 173 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 20, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→38.28 Å / Num. obs: 72134 / % possible obs: 94 % / Redundancy: 3.6 % / Biso Wilson estimate: 20.58 Å2 / Net I/σ(I): 42.6 |
Reflection shell | Resolution: 1.45→1.5 Å / Num. unique obs: 5088 / % possible all: 66.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→38.28 Å / SU ML: 0.1674 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.9858
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.45 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→38.28 Å
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Refine LS restraints |
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LS refinement shell |
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