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Yorodumi- PDB-1szz: Crystal structure of peptide deformylase from Leptospira Interrog... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1szz | ||||||
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Title | Crystal structure of peptide deformylase from Leptospira Interrogans complexed with inhibitor actinonin | ||||||
Components | Peptide deformylase | ||||||
Keywords | HYDROLASE / half-open conformation / BB2 complexed | ||||||
Function / homology | Function and homology information co-translational protein modification / peptide deformylase / peptide deformylase activity / translation / metal ion binding Similarity search - Function | ||||||
Biological species | Leptospira interrogans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Zhou, Z. / Song, X. / Li, Y. / Gong, W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Novel conformational states of peptide deformylase from pathogenic bacterium Leptospira interrogans: implications for population shift Authors: Zhou, Z. / Song, X. / Gong, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1szz.cif.gz | 277.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1szz.ent.gz | 223.6 KB | Display | PDB format |
PDBx/mmJSON format | 1szz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sz/1szz ftp://data.pdbj.org/pub/pdb/validation_reports/sz/1szz | HTTPS FTP |
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-Related structure data
Related structure data | 1sv2C 1vevC 1veyC 1vezC 1rn5 S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 20260.133 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leptospira interrogans (bacteria) / Gene: DEF / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q93LE9, peptide deformylase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-BB2 / #4: 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: 2.86 Å3/Da / Density % sol: 57 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% PEG1k, PEG8k, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 23, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→20 Å / Num. all: 27414 / Num. obs: 23337 / % possible obs: 85.1 % / Observed criterion σ(F): 27414 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 3.3→3.51 Å / % possible all: 35.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RN5 1rn5 Resolution: 3.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.3→20 Å
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Refine LS restraints |
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