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Yorodumi- PDB-7dmo: Crystal structures of two pericyclases catalyzing [4+2] cycloadditions -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dmo | ||||||
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Title | Crystal structures of two pericyclases catalyzing [4+2] cycloadditions | ||||||
Components | Diels-Alderase | ||||||
Keywords | ISOMERASE / [4+2]-pericyclase / BIOSYNTHETIC PROTEIN | ||||||
Function / homology | Isomerases; Intramolecular lyases / isomerase activity / Diels-Alderase phm7 Function and homology information | ||||||
Biological species | Pyrenochaetopsis sp. (fungus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Wang, Z.D. / Chi, C.B. / 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 | 7dmo.cif.gz | 464.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dmo.ent.gz | 376.5 KB | Display | PDB format |
PDBx/mmJSON format | 7dmo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/7dmo ftp://data.pdbj.org/pub/pdb/validation_reports/dm/7dmo | HTTPS FTP |
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-Related structure data
Related structure data | 7dmnSC S: Starting model for refinement C: citing same article (ref.) |
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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: 41752.055 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrenochaetopsis sp. (fungus) / Gene: phm7 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A2Z5XAU0 #2: Water | ChemComp-HOH / | |
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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: 2.72 Å3/Da / Density % sol: 54.8 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.1 M Bis-Tris pH 7.0, 1.36 M Sodium malonate pH 7.0 |
-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: Sep 22, 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→13.43 Å / Num. obs: 179300 / % possible obs: 99.5 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.33 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 3.43 / Num. unique obs: 17930 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7DMN Resolution: 2→13.43 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 21.25 / 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: 97.33 Å2 / Biso mean: 24.8808 Å2 / Biso min: 9.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→13.43 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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