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- PDB-1iic: Crystal Structure of Saccharomyces cerevisiae N-myristoyltransfer... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1iic | ||||||
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Title | Crystal Structure of Saccharomyces cerevisiae N-myristoyltransferase with Bound MyristoylCoA | ||||||
![]() | PEPTIDE N-myristoyltransferase | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() Inactivation, recovery and regulation of the phototransduction cascade / N-terminal peptidyl-glycine N-myristoylation / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Farazi, T.A. / Waksman, G. / Gordon, J.I. | ||||||
![]() | ![]() Title: Structures of Saccharomyces cerevisiae N-myristoyltransferase with bound myristoylCoA and peptide provide insights about substrate recognition and catalysis. Authors: Farazi, T.A. / Waksman, G. / Gordon, J.I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 188 KB | Display | ![]() |
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PDB format | ![]() | 148.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 494.6 KB | Display | ![]() |
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Full document | ![]() | 491 KB | Display | |
Data in XML | ![]() | 21.3 KB | Display | |
Data in CIF | ![]() | 32 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1iidC ![]() 2nmtS S: Starting model for refinement C: citing same article ( |
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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: 49013.973 Da / Num. of mol.: 2 Fragment: N-myristoyltransferase (N-terminal 33 residues deleted) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: NMT / Plasmid: pBB501 / Production host: ![]() ![]() References: UniProt: P14743, glycylpeptide N-tetradecanoyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: PEG 4000, ammonium acetate, sodium cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 10, 2000 / Details: Yale Mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 53396 / Num. obs: 48952 / % possible obs: 91.7 % / Observed criterion σ(F): 2 / Biso Wilson estimate: 20.9 Å2 / Rsym value: 4.8 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2.2→2.28 Å / Mean I/σ(I) obs: 7 / Rsym value: 13.4 / % possible all: 79.59 |
Reflection | *PLUS Num. measured all: 341253 / Rmerge(I) obs: 0.048 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2NMT Resolution: 2.2→27.22 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1973354.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.26 Å2 / ksol: 0.371 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→27.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 5.1 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28.8 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.275 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.232 |