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- PDB-1iyl: Crystal Structure of Candida albicans N-myristoyltransferase with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1iyl | ||||||
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Title | Crystal Structure of Candida albicans N-myristoyltransferase with Non-peptidic Inhibitor | ||||||
![]() | Myristoyl-CoA:Protein N-Myristoyltransferase | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sogabe, S. / Fukami, T.A. / Morikami, K. / Shiratori, Y. / Aoki, Y. / D'Arcy, A. / Winkler, F.K. / Banner, D.W. / Ohtsuka, T. | ||||||
![]() | ![]() Title: Crystal Structures of Candida albicans N-Myristoyltransferase with Two Distinct Inhibitors Authors: Sogabe, S. / Masubuchi, M. / Sakata, K. / Fukami, T.A. / Morikami, K. / Shiratori, Y. / Ebiike, H. / Kawasaki, K. / Aoki, Y. / Shimma, N. / D'Arcy, A. / Winkler, F.K. / Banner, D.W. / Ohtsuka, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 311.9 KB | Display | ![]() |
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PDB format | ![]() | 253.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 585.1 KB | Display | ![]() |
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Full document | ![]() | 690.6 KB | Display | |
Data in XML | ![]() | 45.1 KB | Display | |
Data in CIF | ![]() | 65.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1iykSC 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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Unit cell |
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Components
#1: Protein | Mass: 45421.566 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P30418, glycylpeptide N-tetradecanoyltransferase #2: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.25 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG3350, lithium sulfate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 288 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Nov 28, 1998 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. all: 40711 / Num. obs: 40711 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 3.1 / Num. unique all: 4020 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 50 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1IYK Resolution: 3.2→40 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: B-GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.4476 Å2 / ksol: 0.232096 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.4 Å2 | ||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.31 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
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Refinement | *PLUS Lowest resolution: 40 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 3.2 Å |