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Yorodumi- PDB-3g5k: Structure and activity of human mitochondrial peptide deformylase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g5k | ||||||
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Title | Structure and activity of human mitochondrial peptide deformylase, a novel cancer target | ||||||
Components | Peptide deformylase, mitochondrial | ||||||
Keywords | HYDROLASE / PEPTIDE DEFORMYLASE / ACTINONIN / Iron / Metal-binding / Mitochondrion / Protein biosynthesis / Transit peptide | ||||||
Function / homology | Function and homology information co-translational protein modification / N-terminal protein amino acid modification / peptidyl-methionine modification / peptide deformylase / peptide deformylase activity / translation / positive regulation of cell population proliferation / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Escobar-Alvarez, S. / Goldgur, Y. / Yang, G. / Ouerfelli, O. / Li, Y. / Scheinberg, D.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structure and activity of human mitochondrial peptide deformylase, a novel cancer target Authors: Escobar-Alvarez, S. / Goldgur, Y. / Yang, G. / Ouerfelli, O. / Li, Y. / Scheinberg, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g5k.cif.gz | 170.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g5k.ent.gz | 134.3 KB | Display | PDB format |
PDBx/mmJSON format | 3g5k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3g5k_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 3g5k_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 3g5k_validation.xml.gz | 37 KB | Display | |
Data in CIF | 3g5k_validation.cif.gz | 51.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/3g5k ftp://data.pdbj.org/pub/pdb/validation_reports/g5/3g5k | HTTPS FTP |
-Related structure data
Related structure data | 3g5pC 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 20653.014 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDF, PDF1A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HBH1, peptide deformylase #2: Chemical | ChemComp-BB2 / #3: Chemical | ChemComp-CO / #4: 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: 2.89 Å3/Da / Density % sol: 57.5 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 1 M AMMONIUM PHOSPHATE MONOBASIC, 0.1 M SODIUM CITRATE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97922 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2006 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97922 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→100 Å / Num. obs: 100609 / % possible obs: 100 % / Observed criterion σ(I): 5 / Redundancy: 4.6 % / Rsym value: 0.06 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 5.5 / Rsym value: 0.31 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1ZXZ Resolution: 1.7→35 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.943 / SU ML: 0.051 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.086 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.699 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.741 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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