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Yorodumi- PDB-8jmr: Crystal structure of hinokiresinol synthase in complex with 1,7-b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jmr | ||||||
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Title | Crystal structure of hinokiresinol synthase in complex with 1,7-bis(4-hydroxyphenyl)hepta-1,6-dien-3-one | ||||||
Components |
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Keywords | BIOSYNTHETIC PROTEIN / hinokiresinol / hinokiresinol synthase | ||||||
Function / homology | Phloem protein 2-like / Phloem protein 2 / 1,7-bis(4-hydroxyphenyl)hepta-1,6-dien-3-one / Hinokiresinol synthase alpha subunit / Hinokiresinol synthase beta subunit Function and homology information | ||||||
Biological species | Asparagus officinalis (garden asparagus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Ding, Y. / Ushimaru, R. / Mori, T. / Abe, I. | ||||||
Funding support | 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2023 Title: Structural and Mechanistic Insights into the C-C Bond-Forming Rearrangement Reaction Catalyzed by Heterodimeric Hinokiresinol Synthase. Authors: Ushimaru, R. / Ding, Y. / Mori, T. / Miyamoto, K. / Uchiyama, M. / Abe, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jmr.cif.gz | 105.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jmr.ent.gz | 62.6 KB | Display | PDB format |
PDBx/mmJSON format | 8jmr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jmr_validation.pdf.gz | 752.2 KB | Display | wwPDB validaton report |
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Full document | 8jmr_full_validation.pdf.gz | 752.5 KB | Display | |
Data in XML | 8jmr_validation.xml.gz | 16 KB | Display | |
Data in CIF | 8jmr_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jm/8jmr ftp://data.pdbj.org/pub/pdb/validation_reports/jm/8jmr | HTTPS FTP |
-Related structure data
Related structure data | 8jmqC 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
#1: Protein | Mass: 20176.369 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Asparagus officinalis (garden asparagus) Gene: AoHRSa / Production host: Escherichia coli (E. coli) / References: UniProt: A9CQD3 |
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#2: Protein | Mass: 22212.457 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Asparagus officinalis (garden asparagus) Gene: AoHRSb / Production host: Escherichia coli (E. coli) / References: UniProt: A9CQD5 |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-UR0 / |
#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: 2.2 Å3/Da / Density % sol: 44.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100mM sodium cacodylate trihydrate (pH6.5), 200mM ammonium sulfate, 20% PEG 8000, 2mM inhibitor |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 2, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→46.43 Å / Num. obs: 19260 / % possible obs: 100 % / Redundancy: 22.4 % / Biso Wilson estimate: 28.51 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.243 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.2→2.27 Å / Rmerge(I) obs: 1.234 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1668 / CC1/2: 0.891 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→46.43 Å / SU ML: 0.2467 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.2952 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 27.97 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→46.43 Å
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Refine LS restraints |
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LS refinement shell |
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