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Yorodumi- PDB-7e22: Crystal structure of two pericyclases catalyzing [4+2] cycloaddition -
+Open data
-Basic information
Entry | Database: PDB / ID: 7.0E+22 | ||||||
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Title | Crystal structure of two pericyclases catalyzing [4+2] cycloaddition | ||||||
Components | Diels-Alderase fsa2 | ||||||
Keywords | BIOSYNTHETIC PROTEIN / [4+2]-pericyclase / ISOMERASE | ||||||
Function / homology | Isomerases; Intramolecular lyases / isomerase activity / Equisetin / Diels-Alderase fsa2 Function and homology information | ||||||
Biological species | Fusarium sp. (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å | ||||||
Authors | Chi, C.B. / Wang, Z.D. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crystal structure of two pericyclases catalyzing [4+2] cycloaddition Authors: Chi, C.B. / Wang, Z.D. / Liu, T. / Zhang, Z.Y. / Ma, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e22.cif.gz | 87.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e22.ent.gz | 64.2 KB | Display | PDB format |
PDBx/mmJSON format | 7e22.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7e22_validation.pdf.gz | 763.8 KB | Display | wwPDB validaton report |
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Full document | 7e22_full_validation.pdf.gz | 770.5 KB | Display | |
Data in XML | 7e22_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 7e22_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/7e22 ftp://data.pdbj.org/pub/pdb/validation_reports/e2/7e22 | HTTPS FTP |
-Related structure data
Related structure data | 7dmnS S: Starting model for refinement |
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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
#1: Protein | Mass: 41118.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fusarium sp. (strain FN080326) (fungus) Strain: FN080326 / Gene: fsa2 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A0E4AYE7, Isomerases; Intramolecular lyases |
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#2: Chemical | ChemComp-HVF / |
#3: 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: 2.25 Å3/Da / Density % sol: 45.3 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 28% PEG 2000mme, 0.1 M BIS-TRIS propane pH 6.3, 20 mM TEAOH pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978253 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978253 Å / Relative weight: 1 |
Reflection | Resolution: 2.63→50 Å / Num. obs: 140821 / % possible obs: 99.9 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.63→2.73 Å / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 3.33 / Num. unique obs: 11809 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7DMN Resolution: 2.63→45.88 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.361 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.286 / 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: 154.02 Å2 / Biso mean: 47.149 Å2 / Biso min: 16.9 Å2
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Refinement step | Cycle: final / Resolution: 2.63→45.88 Å
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Refine LS restraints |
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