+Open data
-Basic information
Entry | Database: PDB / ID: 7ei3 | ||||||
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Title | Crystal structure of MasL, a thiolase from Massilia sp. YMA4 | ||||||
Components | Acetyl-CoA C-acyltransferase | ||||||
Keywords | TRANSFERASE / Acetyl-CoA acetyltransferase | ||||||
Function / homology | : Function and homology information | ||||||
Biological species | [Empedobacter] haloabium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å | ||||||
Authors | Lin, C.C. / Huang, K.F. / Yang, Y.L. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Commun Biol / Year: 2022 Title: Integrated omics approach to unveil antifungal bacterial polyynes as acetyl-CoA acetyltransferase inhibitors. Authors: Lin, C.C. / Hoo, S.Y. / Ma, L.T. / Lin, C. / Huang, K.F. / Ho, Y.N. / Sun, C.H. / Lee, H.J. / Chen, P.Y. / Shu, L.J. / Wang, B.W. / Hsu, W.C. / Ko, T.P. / Yang, Y.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ei3.cif.gz | 636.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ei3.ent.gz | 527.2 KB | Display | PDB format |
PDBx/mmJSON format | 7ei3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ei3_validation.pdf.gz | 457.9 KB | Display | wwPDB validaton report |
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Full document | 7ei3_full_validation.pdf.gz | 464.9 KB | Display | |
Data in XML | 7ei3_validation.xml.gz | 68.4 KB | Display | |
Data in CIF | 7ei3_validation.cif.gz | 104.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/7ei3 ftp://data.pdbj.org/pub/pdb/validation_reports/ei/7ei3 | HTTPS FTP |
-Related structure data
Related structure data | 7ei4C 7feaC 4n44S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42607.332 Da / Num. of mol.: 4 / Mutation: V183T Source method: isolated from a genetically manipulated source Source: (gene. exp.) [Empedobacter] haloabium (bacteria) / Gene: E7V67_18950 / Production host: Escherichia coli (E. coli) References: UniProt: A0A5C7BKK5, acetyl-CoA C-acyltransferase #2: 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: 2.77 Å3/Da / Density % sol: 55.54 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2% (v/v) Tacsimate pH 7.0, 16% (w/v) polyethylene glycol 3,350, and 0.1 M HEPES, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Aug 3, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→30 Å / Num. obs: 161164 / % possible obs: 92.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.78→1.84 Å / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 5 / Num. unique obs: 14847 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4N44 Resolution: 1.78→29.9 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.737 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 127.7 Å2 / Biso mean: 21.674 Å2 / Biso min: 11.16 Å2
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Refinement step | Cycle: final / Resolution: 1.78→29.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.781→1.827 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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