[English] 日本語
Yorodumi- PDB-1zxz: X-ray structure of peptide deformylase from Arabidopsis thaliana ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zxz | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray structure of peptide deformylase from Arabidopsis thaliana (AtPDF1A); crystals grown in PEG-5000 MME as precipitant | ||||||
Components | Peptide deformylase, mitochondrial | ||||||
Keywords | HYDROLASE / peptide deformylase / PDF1A / eukaryote / higher plant / Arabidopsis thaliana / zinc ion | ||||||
Function / homology | Function and homology information plant-type cell wall / co-translational protein modification / peptide deformylase / peptide deformylase activity / chloroplast stroma / chloroplast / translation / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Fieulaine, S. / Juillan-Binard, C. / Serero, A. / Dardel, F. / Giglione, C. / Meinnel, T. / Ferrer, J.-L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: The crystal structure of mitochondrial (Type 1A) peptide deformylase provides clear guidelines for the design of inhibitors specific for the bacterial forms Authors: Fieulaine, S. / Juillan-Binard, C. / Serero, A. / Dardel, F. / Giglione, C. / Meinnel, T. / Ferrer, J.-L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1zxz.cif.gz | 91 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1zxz.ent.gz | 68.2 KB | Display | PDB format |
PDBx/mmJSON format | 1zxz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/1zxz ftp://data.pdbj.org/pub/pdb/validation_reports/zx/1zxz | HTTPS FTP |
---|
-Related structure data
Related structure data | 1zy0C 1zy1C 1y6hS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
| ||||||||||
Details | Dimer in the asymmetric unit, but it is unclear whether it is a biological dimer or not |
-Components
#1: Protein | Mass: 22310.689 Da / Num. of mol.: 2 / Fragment: mature protein Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PDF1A / Plasmid: pQE30 derivative / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9FV53, peptide deformylase #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.2 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Crystals grown in PEG-5000 MME as precipitant, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979 Å |
Detector | Type: MARRESEARCH 176mm / Detector: CCD / Date: Jan 30, 2005 |
Radiation | Monochromator: 2 silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 10698 / Num. obs: 10552 / % possible obs: 99 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 13.2 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Y6H Resolution: 2.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|