[English] 日本語
Yorodumi- PDB-3pn4: Crystal structure of Arabidopsis thaliana petide deformylase 1B (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pn4 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) in complex with actinonin (crystallized in PEG-550-MME) | ||||||
Components | Peptide deformylase 1B, chloroplastic | ||||||
Keywords | HYDROLASE/ANTIBIOTIC / peptide deformylase / 1B / PDF / N-terminal excision pathway / NME / induced-fit / HYDROLASE-ANTIBIOTIC complex | ||||||
Function / homology | Function and homology information peptide deformylase / peptide deformylase activity / plastid / chloroplast stroma / chloroplast / translation / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å | ||||||
Authors | Fieulaine, S. / Meinnel, T. / Giglione, C. | ||||||
Citation | Journal: Plos Biol. / Year: 2011 Title: Trapping conformational States along ligand-binding dynamics of Peptide deformylase: the impact of induced fit on enzyme catalysis. Authors: Fieulaine, S. / Boularot, A. / Artaud, I. / Desmadril, M. / Dardel, F. / Meinnel, T. / Giglione, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3pn4.cif.gz | 93.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3pn4.ent.gz | 69.9 KB | Display | PDB format |
PDBx/mmJSON format | 3pn4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/3pn4 ftp://data.pdbj.org/pub/pdb/validation_reports/pn/3pn4 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3m6oC 3m6pC 3m6qC 3m6rC 3o3jC 3pn2SC 3pn3C 3pn5C 3pn6C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21976.232 Da / Num. of mol.: 1 / Fragment: UNP residues 83-273 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DEF2, PDF1B / Production host: Escherichia coli (E. coli) / Strain (production host): Jm101Tr / References: UniProt: Q9FUZ2, peptide deformylase | ||
---|---|---|---|
#2: Chemical | ChemComp-BB2 / | ||
#3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.75 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% PEG-550-MME, Zinc sulfate 25mM, 70mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 18505 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rsym value: 0.059 / Net I/σ(I): 18.95 |
Reflection shell | Resolution: 1.9→2.02 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 4.14 / Rsym value: 0.335 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: PDB ENTRY 3PN2 Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.135 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.274 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→40 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -0.6212 Å / Origin y: 16.2822 Å / Origin z: 59.9533 Å
|