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Yorodumi- PDB-1s17: Identification of Novel Potent Bicyclic Peptide Deformylase Inhibitors -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s17 | ||||||
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Title | Identification of Novel Potent Bicyclic Peptide Deformylase Inhibitors | ||||||
Components | Peptide deformylase | ||||||
Keywords | HYDROLASE / peptide deformylase inhibitor / rational drug design / antibiotic / protein-ligand 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 | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Molteni, V. / He, X. / Nabakka, J. / Yang, K. / Kreusch, A. / Gordon, P. / Bursulaya, B. / Ryder, N.S. / Goldberg, R. / He, Y. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2004 Title: Identification of novel potent bicyclic peptide deformylase inhibitors Authors: Molteni, V. / He, X. / Nabakka, J. / Yang, K. / Kreusch, A. / Gordon, P. / Bursulaya, B. / Warner, I. / Shin, T. / Biorac, T. / Ryder, N.S. / Goldberg, R. / Doughty, J. / He, Y. #1: Journal: J.Mol.Biol. / Year: 2003 Title: Structure analysis of peptide deformylases from Streptococcus pneumoniae, Staphylococcus aureus, Thermotoga maritima and Pseudomonas aeruginosa: snapshots of the oxygen sensitivity of peptide deformylase Authors: Kreusch, A. / Spraggon, G. / Lee, C.C. / Klock, H. / McMullan, D. / Ng, K. / Shin, T. / Vincent, J. / Warner, I. / Ericson, C. / Lesley, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s17.cif.gz | 86.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s17.ent.gz | 64.3 KB | Display | PDB format |
PDBx/mmJSON format | 1s17.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s1/1s17 ftp://data.pdbj.org/pub/pdb/validation_reports/s1/1s17 | HTTPS FTP |
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-Related structure data
Related structure data | 1n5nS 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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2 |
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Unit cell |
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Details | the functional unit is a monomer |
-Components
#1: Protein | Mass: 20866.818 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: DEF, PA0019 / Plasmid: pMH4 / Production host: Escherichia coli (E. coli) / Strain (production host): Genehogs / References: UniProt: Q9I7A8, peptide deformylase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #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: 2.35 Å3/Da / Density % sol: 47.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: PEG 3350, MgSO4, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 108 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 11, 2002 / Details: mirror |
Radiation | Monochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→25.68 Å / Num. obs: 28955 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17 % / Biso Wilson estimate: 17.2 Å2 / Rsym value: 0.07 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.95→2.01 Å / Rmerge(I) obs: 0.415 / Num. unique all: 1955 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1N5N Resolution: 1.95→25.68 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 27 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→25.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.05 Å / Rfactor Rfree error: 0.018
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