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Yorodumi- PDB-1lru: Crystal Structure of E.coli Peptide Deformylase Complexed with An... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lru | ||||||
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Title | Crystal Structure of E.coli Peptide Deformylase Complexed with Antibiotic Actinonin | ||||||
Components | PEPTIDE DEFORMYLASE | ||||||
Keywords | HYDROLASE / ACTINONIN / INHIBITION / POLYPEPTIDE DEFORMYLASE | ||||||
Function / homology | Function and homology information co-translational protein modification / peptide deformylase / peptide deformylase activity / ferrous iron binding / ribosome binding / hydrolase activity / translation / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SIRAS / Resolution: 2.1 Å | ||||||
Authors | Guilloteau, J.-P. / Mathieu, M. / Giglione, C. / Blanc, V. / Dupuy, A. / Chevrier, M. / Gil, P. / Famechon, A. / Meinnel, T. / Mikol, V. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lru.cif.gz | 122.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lru.ent.gz | 95.3 KB | Display | PDB format |
PDBx/mmJSON format | 1lru.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/1lru ftp://data.pdbj.org/pub/pdb/validation_reports/lr/1lru | 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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3 |
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4 |
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Unit cell |
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Details | the biological unit is the monomer. There are three monomers in the asymetric unit. |
-Components
#1: Protein | Mass: 19226.248 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6K3, 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: 2.6 Å3/Da / Density % sol: 54.63 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.5M (NH4)2SO4, 28%PEG400, pH 6.0, 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: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å |
Detector | Type: MAC Science DIP-2000 / Detector: IMAGE PLATE / Date: Apr 14, 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: 2.1→15 Å / Num. all: 34394 / Num. obs: 34394 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rsym value: 0.076 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 2.3 % / Num. unique all: 3037 / Rsym value: 0.251 / % possible all: 83.7 |
Reflection | *PLUS Lowest resolution: 15 Å / Rmerge(I) obs: 0.076 |
Reflection shell | *PLUS Highest resolution: 2.1 Å / % possible obs: 83.7 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 5 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.1→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.1→15 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.1 Å / Rfactor obs: 0.24 / Rfactor Rwork: 0.24 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |