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- PDB-3pn2: Crystal structure of Arabidopsis thaliana petide deformylase 1B (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3pn2 | ||||||
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Title | Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) (crystallized in PEG-550-MME) | ||||||
![]() | Peptide deformylase 1B, chloroplastic | ||||||
![]() | HYDROLASE / peptide deformylase / 1B / PDF / N-terminal excision pathway / NME / induced-fit | ||||||
Function / homology | ![]() peptide deformylase / peptide deformylase activity / plastid / chloroplast stroma / chloroplast / translation / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fieulaine, S. / Meinnel, T. / Giglione, C. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93.5 KB | Display | ![]() |
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PDB format | ![]() | 70.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.3 KB | Display | ![]() |
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Full document | ![]() | 429.8 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 17.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3m6oSC ![]() 3m6pC ![]() 3m6qC ![]() 3m6rC ![]() 3o3jC ![]() 3pn3C ![]() 3pn4C ![]() 3pn5C ![]() 3pn6C C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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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.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% PEG-550-MME, Zinc sulfate 75mM, 70mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / 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: 2→30 Å / Num. obs: 15978 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rsym value: 0.05 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2→2.12 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.65 / Num. unique all: 4882 / Rsym value: 0.409 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3M6O Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.985 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 45.124 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.053 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -0.4386 Å / Origin y: 15.3112 Å / Origin z: 60.6058 Å
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