+Open data
-Basic information
Entry | Database: PDB / ID: 8bxl | ||||||
---|---|---|---|---|---|---|---|
Title | Patulin Synthase from Penicillium expansum | ||||||
Components | Patulin synthase | ||||||
Keywords | FLAVOPROTEIN / Oxidoreductase / GMC-type flavoprotein / Biocatalysis | ||||||
Function / homology | Function and homology information patulin biosynthetic process / Oxidoreductases; Acting on the CH-OH group of donors / polyketide synthase activity / oxidoreductase activity, acting on CH-OH group of donors / vacuole / extracellular matrix / flavin adenine dinucleotide binding / cell cortex / oxidoreductase activity / extracellular region Similarity search - Function | ||||||
Biological species | Penicillium expansum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Tjallinks, G. / Boverio, A. / Rozeboom, H.J. / Fraaije, M.W. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Febs J. / Year: 2023 Title: Structure elucidation and characterization of patulin synthase, insights into the formation of a fungal mycotoxin. Authors: Tjallinks, G. / Boverio, A. / Maric, I. / Rozeboom, H. / Arentshorst, M. / Visser, J. / Ram, A.F.J. / Mattevi, A. / Fraaije, M.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8bxl.cif.gz | 718 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8bxl.ent.gz | 588.1 KB | Display | PDB format |
PDBx/mmJSON format | 8bxl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/8bxl ftp://data.pdbj.org/pub/pdb/validation_reports/bx/8bxl | HTTPS FTP |
---|
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||||||||||||||||||||||
3 |
| ||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS ensembles :
|
-Components
-Protein , 1 types, 6 molecules BCDAFE
#1: Protein | Mass: 68198.242 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Penicillium expansum (fungus) / Gene: patE, PEX2_082770 / Production host: Aspergillus niger (mold) References: UniProt: A0A075TRK9, Oxidoreductases; Acting on the CH-OH group of donors |
---|
-Sugars , 3 types, 30 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / |
---|
-Non-polymers , 4 types, 1012 molecules
#4: Chemical | ChemComp-FAD / #6: Chemical | ChemComp-PEG / #7: Chemical | ChemComp-GOL / #8: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.08 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: Calcium chloride, PEG6000 and sodium acetate pH 5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 26, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9655 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→48.74 Å / Num. obs: 179872 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.978 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.064 / Rrim(I) all: 0.168 / Χ2: 0.81 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.4→2.44 Å / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 1.113 / Num. measured all: 60753 / Num. unique obs: 8892 / CC1/2: 0.72 / Rpim(I) all: 0.47 / Rrim(I) all: 1.211 / Χ2: 0.48 / Net I/σ(I) obs: 3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→48.74 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.163 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.326 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 37.378 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.4→48.74 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|