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- PDB-1lry: Crystal Structure of P. aeruginosa Peptide Deformylase Complexed ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1lry | ||||||
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Title | Crystal Structure of P. aeruginosa Peptide Deformylase Complexed with Antibiotic Actinonin | ||||||
![]() | PEPTIDE deformylase | ||||||
![]() | HYDROLASE / ACTINONIN / INHIBITION / POLYPEPTIDE DEFORMYLASE | ||||||
Function / homology | ![]() co-translational protein modification / peptide deformylase / peptide deformylase activity / translation / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Guilloteau, J.-P. / Mathieu, M. / Giglione, C. / Blanc, V. / Dupuy, A. / Chevrier, M. / Gil, P. / Famechon, A. / Meinnel, T. / Mikol, V. | ||||||
![]() | ![]() Title: The crystal structures of four peptide deformylases bound to the antibiotic actinonin reveal two distinct types: a platform for the structure-based design of antibacterial agents. Authors: Guilloteau, J.P. / Mathieu, M. / Giglione, C. / Blanc, V. / Dupuy, A. / Chevrier, M. / Gil, P. / Famechon, A. / Meinnel, T. / Mikol, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.4 KB | Display | ![]() |
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PDB format | ![]() | 35.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | the biological assembly is the monomer |
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Components
#1: Protein | Mass: 19259.961 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-BB2 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 57.34 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 32% PEG6000, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 19 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAC Science DIP-2000 / Detector: IMAGE PLATE / Date: Oct 22, 1997 |
Radiation | Monochromator: Ni MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→15 Å / Num. all: 7756 / Num. obs: 7756 / % possible obs: 85.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rsym value: 0.088 |
Reflection shell | Resolution: 2.6→2.69 Å / Num. unique all: 580 / Rsym value: 0.246 / % possible all: 85.3 |
Reflection | *PLUS Lowest resolution: 15 Å / Rmerge(I) obs: 0.088 |
Reflection shell | *PLUS % possible obs: 85.3 % / Rmerge(I) obs: 0.246 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.6→15 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 15 Å / Rfactor obs: 0.221 / Rfactor Rwork: 0.221 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS Type: x_bond_d / Dev ideal: 0.007 |