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Yorodumi- PDB-3o3j: Crystal structure of Arabidopsis thaliana peptide deformylase 1B ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o3j | ||||||
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Title | Crystal structure of Arabidopsis thaliana peptide deformylase 1B (AtPDF1B) in complex with inhibitor 6b | ||||||
Components | Peptide deformylase 1B | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / peptide deformylase / 1B / PDF / N-terminal excision pathway / NME / Arabidopsis thaliana / induced-fit / Hydrolase / HYDROLASE-HYDROLASE INHIBITOR 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 / MOLECULAR REPLACEMENT / Resolution: 3 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o3j.cif.gz | 91.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o3j.ent.gz | 69.2 KB | Display | PDB format |
PDBx/mmJSON format | 3o3j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/3o3j ftp://data.pdbj.org/pub/pdb/validation_reports/o3/3o3j | HTTPS FTP |
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-Related structure data
Related structure data | 3m6oSC 3m6pC 3m6qC 3m6rC 3pn2C 3pn3C 3pn4C 3pn5C 3pn6C 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21976.232 Da / Num. of mol.: 1 / Fragment: residues 1-193 / Mutation: R118K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: def / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): Jm101Tr / References: UniProt: Q9FUZ2, peptide deformylase | ||||
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#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-BB4 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.84 % / Description: THE FILE CONTAINS FRIEDEL PAIRS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: PEG550MME, ZnSO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å |
Detector | Date: Oct 15, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3→35 Å / Num. all: 9287 / Num. obs: 9113 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rsym value: 0.046 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 3→3.18 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 3 / Num. unique all: 1460 / Rsym value: 0.241 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3M6O Resolution: 3→28.75 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.854 / SU B: 37.362 / SU ML: 0.403 / Cross valid method: THROUGHOUT / ESU R Free: 0.496 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FILE CONTAINS FRIEDEL PAIRS.
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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: 73.294 Å2
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Refinement step | Cycle: LAST / Resolution: 3→28.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.002→3.079 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 0.9161 Å / Origin y: 16.0247 Å / Origin z: -23.4031 Å
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