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Yorodumi- PDB-2p6f: Crystal structures of Saccharomyces cerevisiae N-myristoyltransfe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p6f | ||||||
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Title | Crystal structures of Saccharomyces cerevisiae N-myristoyltransferase with bound myristoyl-CoA and inhibitors | ||||||
Components | Glycylpeptide N-tetradecanoyltransferase | ||||||
Keywords | TRANSFERASE / antifungal drug / non-peptidic inhibitor | ||||||
Function / homology | Function and homology information Inactivation, recovery and regulation of the phototransduction cascade / N-terminal peptidyl-glycine N-myristoylation / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Wu, J. / Ding, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Crystal structures of Saccharomyces cerevisiae N-myristoyltransferase with bound myristoyl-CoA and inhibitors reveal the functional roles of the N-terminal region. Authors: Wu, J. / Tao, Y. / Zhang, M. / Howard, M.H. / Gutteridge, S. / Ding, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p6f.cif.gz | 966 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p6f.ent.gz | 805.6 KB | Display | PDB format |
PDBx/mmJSON format | 2p6f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/2p6f ftp://data.pdbj.org/pub/pdb/validation_reports/p6/2p6f | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 52911.383 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: 850892 / Plasmid: pBX3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS References: UniProt: P14743, glycylpeptide N-tetradecanoyltransferase #2: Chemical | ChemComp-MYA / #3: Chemical | ChemComp-GN8 / ( |
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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: 2.88 Å3/Da / Density % sol: 57.23 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: 2.6M ammonium salphate, 20mM HEPES, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 12, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 65374 / % possible obs: 97.5 % / Redundancy: 3 % / Rmerge(I) obs: 0.154 / Rsym value: 0.154 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.329 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→20 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.818 / SU B: 73.838 / SU ML: 0.572 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.642 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 37.195 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.179 Å / Total num. of bins used: 20
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