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Yorodumi- PDB-4mfp: The crystal structure of acyltransferase in complex with decanoyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mfp | |||||||||
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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: 2.15 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 | 4mfp.cif.gz | 97.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mfp.ent.gz | 71.2 KB | Display | PDB format |
PDBx/mmJSON format | 4mfp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mfp_validation.pdf.gz | 807.3 KB | Display | wwPDB validaton report |
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Full document | 4mfp_full_validation.pdf.gz | 814.1 KB | Display | |
Data in XML | 4mfp_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 4mfp_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mf/4mfp ftp://data.pdbj.org/pub/pdb/validation_reports/mf/4mfp | HTTPS FTP |
-Related structure data
Related structure data | 4mfjSC 4mfkC 4mflC 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-MAN / |
#7: Sugar | ChemComp-GCS / |
-Non-polymers , 4 types, 258 molecules
#3: Chemical | ChemComp-COA / | ||||
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#4: Chemical | #8: Chemical | ChemComp-DKA / | #9: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | ABOUT THE BOND DISTANCE BETWEEN N2 (GCS 503) AND C1 (DKA 504) IS HIGHER THAN CUTOFF DISTANCE, THE ...ABOUT THE BOND DISTANCE BETWEEN N2 (GCS 503) AND C1 (DKA 504) IS HIGHER THAN CUTOFF DISTANCE, THE DEPOSITORS |
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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: 3.18 Å3/Da / Density % sol: 61.27 % |
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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: 2.15→30 Å / Num. all: 26394 / Num. obs: 26394 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.15→2.23 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MFJ Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.658 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.185 / ESU R Free: 0.164 / 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: 40.945 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.153→2.209 Å / Total num. of bins used: 20
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