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Yorodumi- PDB-7dmn: Crystal structure of two pericyclases catalyzing [4+2] cycloaddition -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dmn | ||||||
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Title | Crystal structure of two pericyclases catalyzing [4+2] cycloaddition | ||||||
Components | Diels-Alderase fsa2 | ||||||
Keywords | ISOMERASE / [4+2]-pericyclase / BIOSYNTHETIC PROTEIN | ||||||
Function / homology | Isomerases; Intramolecular lyases / isomerase activity / Diels-Alderase fsa2 Function and homology information | ||||||
Biological species | Fusarium sp. (fungus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Chi, C.B. / Wang, Z.D. / Liu, T. / Zhang, Z.Y. / Ma, M. | ||||||
Funding support | China, 1items
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Citation | Journal: Acs Omega / Year: 2021 Title: Crystal Structures of Fsa2 and Phm7 Catalyzing [4 + 2] Cycloaddition Reactions with Reverse Stereoselectivities in Equisetin and Phomasetin Biosynthesis. Authors: Chi, C. / Wang, Z. / Liu, T. / Zhang, Z. / Zhou, H. / Li, A. / Jin, H. / Jia, H. / Yin, F. / Yang, D. / Ma, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dmn.cif.gz | 91.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dmn.ent.gz | 67.6 KB | Display | PDB format |
PDBx/mmJSON format | 7dmn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dmn_validation.pdf.gz | 441.5 KB | Display | wwPDB validaton report |
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Full document | 7dmn_full_validation.pdf.gz | 444.7 KB | Display | |
Data in XML | 7dmn_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 7dmn_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/7dmn ftp://data.pdbj.org/pub/pdb/validation_reports/dm/7dmn | HTTPS FTP |
-Related 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 | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 40.06 % |
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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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.540562 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Nov 11, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.540562 Å / Relative weight: 1 |
Reflection | Resolution: 2→13.61 Å / Num. obs: 23436 / % possible obs: 99.3 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 26.86 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 7.15 / Num. unique obs: 2349 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Se-Fsa2 Resolution: 2→13.61 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.682 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.167 / 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: 108.41 Å2 / Biso mean: 20.263 Å2 / Biso min: 2.78 Å2
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Refinement step | Cycle: final / Resolution: 2→13.61 Å
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LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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