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Yorodumi- PDB-4mfk: The crystal structure of acyltransferase in complex with decanoyl-CoA -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mfk | ||||||
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Title | The crystal structure of acyltransferase in complex with decanoyl-CoA | ||||||
Components | Putative uncharacterized protein tcp24 | ||||||
Keywords | TRANSFERASE / GNAT / acyltransferase / acyl-CoA | ||||||
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 | 4mfk.cif.gz | 95.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mfk.ent.gz | 70.1 KB | Display | PDB format |
PDBx/mmJSON format | 4mfk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mf/4mfk ftp://data.pdbj.org/pub/pdb/validation_reports/mf/4mfk | HTTPS FTP |
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-Related structure data
Related structure data | 4mfjSC 4mflC 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
#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: Chemical | ChemComp-MFK / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62.08 % |
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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: BL13C1 / Wavelength: 0.97622 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Oct 23, 2012 |
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: 1.9→30 Å / Num. all: 39938 / Num. obs: 37919 / % 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: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.58 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.114 / ESU R Free: 0.114 / 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: 29.624 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: 1.898→1.948 Å / Total num. of bins used: 20
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