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- PDB-4je8: Crystal structure of a human-like mitochondrial peptide deformyla... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4je8 | ||||||
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Title | Crystal structure of a human-like mitochondrial peptide deformylase in complex with Met-Ala-Ser | ||||||
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![]() | HYDROLASE/PEPTIDE / peptide deformylase / mitochondrial / HYDROLASE-PEPTIDE complex | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Fieulaine, S. / Meinnel, T. / Giglione, C. | ||||||
![]() | ![]() Title: Understanding the highly efficient catalysis of prokaryotic peptide deformylases by shedding light on the determinants specifying the low activity of the human counterpart. Authors: Fieulaine, S. / Desmadril, M. / 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 | ![]() | 170.8 KB | Display | ![]() |
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PDB format | ![]() | 134.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.3 KB | Display | ![]() |
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Full document | ![]() | 453.6 KB | Display | |
Data in XML | ![]() | 20.3 KB | Display | |
Data in CIF | ![]() | 28.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4je6C ![]() 4je7C ![]() 1zxzS 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: 22372.736 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 79-267 / Mutation: G47C, L112E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 307.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemical product #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.21 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 5-15% PEG 5000 MME, 100mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Date: Apr 9, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 16326 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rsym value: 0.084 / Net I/σ(I): 11.68 |
Reflection shell | Resolution: 2.39→2.54 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.03 / Rsym value: 0.386 / % possible all: 97.2 |
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Processing
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Refinement | Starting model: PDB entry 1ZXZ Resolution: 2.4→46.68 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.916 / SU B: 16.219 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.424 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: RIGID BODY HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
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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: 44.227 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→46.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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