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Yorodumi- PDB-4mfl: The crystal structure of acyltransferase in complex with decanoyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mfl | |||||||||
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Title | The crystal structure of acyltransferase in complex with decanoyl-CoA and Tei pseudoaglycone | |||||||||
Components |
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Keywords | Transferase/Antibiotic / GNAT / acyltransferase / acyl-CoA / Transferase-Antibiotic complex | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Actinoplanes teichomyceticus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Lyu, S.Y. / Liu, Y.C. / Chang, C.Y. / Huang, C.J. / Li, T.L. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mfl.cif.gz | 99.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mfl.ent.gz | 72.3 KB | Display | PDB format |
PDBx/mmJSON format | 4mfl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mfl_validation.pdf.gz | 832.5 KB | Display | wwPDB validaton report |
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Full document | 4mfl_full_validation.pdf.gz | 838.1 KB | Display | |
Data in XML | 4mfl_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 4mfl_validation.cif.gz | 29.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mf/4mfl ftp://data.pdbj.org/pub/pdb/validation_reports/mf/4mfl | HTTPS FTP |
-Related structure data
Related structure data | 4mfjSC 4mfkC 4mfpC 4mfqC 4mfzC 4q36C 4q38C 4mfs 4mft 4mfw 4mfx 4mfy 4mg0 4mg1 S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 39204.344 Da / Num. of mol.: 1 / Mutation: H196A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Actinoplanes teichomyceticus (bacteria) Gene: tcp24 / Production host: Escherichia coli (E. coli) References: UniProt: Q70AY4, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
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#2: Protein/peptide | |
-Sugars , 3 types, 3 molecules
#5: Sugar | ChemComp-NAG / |
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#6: Sugar | ChemComp-GCS / |
#7: Sugar | ChemComp-MAN / |
-Non-polymers , 3 types, 367 molecules
#3: Chemical | #4: Chemical | ChemComp-MFK / | #8: 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: 3.14 Å3/Da / Density % sol: 60.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1mM MES, 0.2M ammonium sulphate, 30%(V/V) PEG5000 MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Mar 19, 2013 |
Radiation | Monochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 37841 / Num. obs: 37841 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MFJ Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.638 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.121 / ESU R Free: 0.119 / 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 max: 115.62 Å2 / Biso mean: 35.1449 Å2 / Biso min: 15.41 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.899→1.949 Å / Total num. of bins used: 20
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