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Yorodumi- PDB-4je6: Crystal structure of a human-like mitochondrial peptide deformylase -
+Open data
-Basic information
Entry | Database: PDB / ID: 4je6 | ||||||
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Title | Crystal structure of a human-like mitochondrial peptide deformylase | ||||||
Components | Peptide deformylase 1A, chloroplastic/mitochondrial | ||||||
Keywords | HYDROLASE / peptide deformylase / mitochondrial | ||||||
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 / rigid body / Resolution: 2 Å | ||||||
Authors | Fieulaine, S. / Meinnel, T. / Giglione, C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4je6.cif.gz | 169.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4je6.ent.gz | 132 KB | Display | PDB format |
PDBx/mmJSON format | 4je6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/4je6 ftp://data.pdbj.org/pub/pdb/validation_reports/je/4je6 | HTTPS FTP |
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-Related structure data
Related structure data | 4je7C 4je8C 1zxzS C: citing same article (ref.) S: Starting model for refinement |
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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: 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.) Arabidopsis thaliana (thale cress) / Gene: At1g15390, def, DEF1, F9L1.34, F9L1_34, PDF1A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FV53, peptide deformylase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.13 % |
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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 | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.94→50 Å / Num. all: 31669 / Num. obs: 30924 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Net I/σ(I): 17.52 |
Reflection shell | Resolution: 1.94→2.04 Å / Redundancy: 4 % / Mean I/σ(I) obs: 8.22 / Rsym value: 0.163 / % possible all: 85.6 |
-Processing
Software |
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Refinement | Method to determine structure: rigid body Starting model: PDB entry 1ZXZ Resolution: 2→28.96 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.262 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.136 / 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: 14.242 Å2
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Refinement step | Cycle: LAST / Resolution: 2→28.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 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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