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Yorodumi- PDB-7wgh: Crystal structure of AflSQS from Aspergillus flavus in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wgh | ||||||
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Title | Crystal structure of AflSQS from Aspergillus flavus in complex with FSPP | ||||||
Components | Squalene synthase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / isoprenoid synthase | ||||||
Function / homology | Function and homology information squalene synthase / farnesyl-diphosphate farnesyltransferase activity / squalene synthase activity / sterol biosynthetic process / membrane => GO:0016020 Similarity search - Function | ||||||
Biological species | Aspergillus flavus (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å | ||||||
Authors | Shang, N. / Liu, W.D. / Chen, C.C. / Guo, R.T. | ||||||
Funding support | 1items
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Citation | Journal: Acs Omega / Year: 2022 Title: A Structural and Bioinformatics Investigation of a Fungal Squalene Synthase and Comparisons with Other Membrane Proteins. Authors: Malwal, S.R. / Shang, N. / Liu, W. / Li, X. / Zhang, L. / Chen, C.C. / Guo, R.T. / Oldfield, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wgh.cif.gz | 91.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wgh.ent.gz | 67.3 KB | Display | PDB format |
PDBx/mmJSON format | 7wgh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wgh_validation.pdf.gz | 797.5 KB | Display | wwPDB validaton report |
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Full document | 7wgh_full_validation.pdf.gz | 800.4 KB | Display | |
Data in XML | 7wgh_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 7wgh_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/7wgh ftp://data.pdbj.org/pub/pdb/validation_reports/wg/7wgh | HTTPS FTP |
-Related structure data
Related structure data | 7wgiC 1ezfS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 54750.973 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus flavus (mold) Gene: BDV35DRAFT_364291, CA14_004282, F9C07_2287043, G4B11_012149 Plasmid: pET46 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A364LX79, squalene synthase | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.25 % / Mosaicity: 0.435 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.1 M NaH2PO4, 0.5 M K2HPO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.9998 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 27, 2019 |
Radiation | Monochromator: LN2 cooled Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9998 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→25 Å / Num. obs: 30779 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 49.88 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.36→2.44 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.834 / Num. unique obs: 3031 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EZF Resolution: 2.36→24.55 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.77 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 129.7 Å2 / Biso mean: 55.33 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.36→24.55 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %
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