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- PDB-4mfz: The crystal structure of acyltransferase in complex with decanoyl-CoA -
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Open data
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Basic information
Entry | Database: PDB / ID: 4mfz | ||||||
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Title | The crystal structure of acyltransferase in complex with decanoyl-CoA | ||||||
![]() | Dbv8 protein | ||||||
![]() | TRANSFERASE / GNAT / acyltransferase / acyl-CoA | ||||||
Function / homology | ![]() Aminopeptidase - #120 / N-acyltransferase, N-terminal domain / GNAT-like C-terminal domain / N-acyltransferase N-terminal domain / GNAT-like C-terminal domain / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lyu, S.Y. / Liu, Y.C. / Chang, C.Y. / Huang, C.J. / Li, T.L. | ||||||
![]() | ![]() Title: Multiple complexes of long aliphatic N-acyltransferases lead to synthesis of 2,6-diacylated/2-acyl-substituted glycopeptide antibiotics, effectively killing vancomycin-resistant enterococcus Authors: Lyu, S.Y. / Liu, Y.C. / Chang, C.Y. / Huang, C.J. / Chiu, Y.H. / Huang, C.M. / Hsu, N.S. / Lin, K.H. / Wu, C.J. / Tsai, M.D. / Li, T.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.5 KB | Display | ![]() |
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PDB format | ![]() | 63.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 759.6 KB | Display | ![]() |
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Full document | ![]() | 766 KB | Display | |
Data in XML | ![]() | 17.6 KB | Display | |
Data in CIF | ![]() | 25.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4mfjSC ![]() 4mfkC ![]() 4mflC ![]() 4mfpC ![]() 4mfqC ![]() 4q36C ![]() 4q38C 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 38585.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q7WZ83, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
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#2: Chemical | ChemComp-MFK / |
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M sodium cacodylate, 0.2M sodium acetate, 30%(V/V) PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2009 |
Radiation | Monochromator: Horizontally Focusing Single Crystal Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 19900 / Num. obs: 19900 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.1→2.18 Å / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4MFJ Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.911 / SU B: 5.548 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.242 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 25.643 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.098→2.152 Å / Total num. of bins used: 20
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