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Yorodumi- PDB-7y47: Crystal structure of bifunctional miltiradiene synthase from sela... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7y47 | ||||||
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Title | Crystal structure of bifunctional miltiradiene synthase from selaginella moellendorffii that complexed with GGPP | ||||||
Components | Bifunctional diterpene synthase, chloroplastic | ||||||
Keywords | PLANT PROTEIN / bifunctional terpnen synthase / CPP / miltiradiene | ||||||
Function / homology | Function and homology information miltiradiene synthase / miltiradiene synthase activity / miltiradiene biosynthetic process / 5alpha,9alpha,10beta-labda-8(20),13-dien-15-yl diphosphate catabolic process / 5alpha,9alpha,10beta-labda-8(20),13-dien-15-yl diphosphate biosynthetic process / copalyl diphosphate synthase activity / copalyl diphosphate synthase / diterpenoid biosynthetic process / terpene synthase activity / chloroplast / magnesium ion binding Similarity search - Function | ||||||
Biological species | Selaginella moellendorffii (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Ma, X. / Tao, Y. / Jiang, T. | ||||||
Funding support | China, 1items
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Citation | Journal: Plant Biotechnol J / Year: 2023 Title: Structural and mechanistic insights into the precise product synthesis by a bifunctional miltiradiene synthase. Authors: Tong, Y. / Ma, X. / Hu, T. / Chen, K. / Cui, G. / Su, P. / Xu, H. / Gao, W. / Jiang, T. / Huang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y47.cif.gz | 193 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y47.ent.gz | 135 KB | Display | PDB format |
PDBx/mmJSON format | 7y47.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7y47_validation.pdf.gz | 1020.4 KB | Display | wwPDB validaton report |
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Full document | 7y47_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7y47_validation.xml.gz | 30.7 KB | Display | |
Data in CIF | 7y47_validation.cif.gz | 44.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/7y47 ftp://data.pdbj.org/pub/pdb/validation_reports/y4/7y47 | HTTPS FTP |
-Related structure data
Related structure data | 7watSC S: Starting model for refinement 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: 91542.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The SmMDS protein comes from BAL41682.1. / Source: (gene. exp.) Selaginella moellendorffii (plant) / Gene: MDS Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: G9MAN7 |
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#2: Chemical | ChemComp-IMD / |
#3: Chemical | ChemComp-GRG / |
#4: 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: 2.47 Å3/Da / Density % sol: 50.12 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES (pH 6.5) 22% (v/v) PEG2000 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 31123 / % possible obs: 96.44 % / Redundancy: 11.4 % / Biso Wilson estimate: 35.86 Å2 / Rpim(I) all: 0.071 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.5→2.54 Å / Num. unique obs: 1596 / CC1/2: 0.717 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7WAT Resolution: 2.5→48.31 Å / SU ML: 0.2648 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5339 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: 45.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→48.31 Å
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Refine LS restraints |
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LS refinement shell |
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