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Yorodumi- PDB-7ei4: Crystal structure of MasL in complex with a novel covalent inhibi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ei4 | ||||||
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Title | Crystal structure of MasL in complex with a novel covalent inhibitor, collimonin C | ||||||
Components | Acetyl-CoA C-acyltransferase | ||||||
Keywords | TRANSFERASE/INHIBITOR / Acetyl-CoA acetyltransferase / TRANSFERASE-INHIBITOR complex | ||||||
Function / homology | Chem-J3U / : Function and homology information | ||||||
Biological species | [Empedobacter] haloabium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.66 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 | 7ei4.cif.gz | 641.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ei4.ent.gz | 530.6 KB | Display | PDB format |
PDBx/mmJSON format | 7ei4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ei4_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7ei4_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7ei4_validation.xml.gz | 72 KB | Display | |
Data in CIF | 7ei4_validation.cif.gz | 107.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/7ei4 ftp://data.pdbj.org/pub/pdb/validation_reports/ei/7ei4 | HTTPS FTP |
-Related structure data
Related structure data | 7ei3C 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: Chemical | ChemComp-J3U / ( #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.51 Å3/Da / Density % sol: 51.02 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% (w/v) polyethylene glycol 3,350 and 0.2 M tri-lithium citrate, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Aug 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→30 Å / Num. obs: 197431 / % possible obs: 99.4 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.66→1.72 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2 / Num. unique obs: 18672 / % possible all: 94.4 |
-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: 1.66→29.22 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.752 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.078 / 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: 93.95 Å2 / Biso mean: 18.347 Å2 / Biso min: 4.68 Å2
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Refinement step | Cycle: final / Resolution: 1.66→29.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.66→1.701 Å / Rfactor Rfree error: 0
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