+Open data
-Basic information
Entry | Database: PDB / ID: 7bux | |||||||||||||||
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Title | Eucommia ulmoides FPS1 | |||||||||||||||
Components | FPS2 | |||||||||||||||
Keywords | PLANT PROTEIN / Prenyltransferase / Polyisoprene | |||||||||||||||
Function / homology | Function and homology information transferase activity, transferring alkyl or aryl (other than methyl) groups / isoprenoid biosynthetic process Similarity search - Function | |||||||||||||||
Biological species | Eucommia ulmoides (plant) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||||||||
Authors | Kajiura, H. / Yoshizawa, T. / Tokumoto, Y. / Suzuki, N. / Takeno, S. / Takeno, K.J. / Yamashita, T. / Tanaka, S. / Kaneko, Y. / Fujiyama, K. ...Kajiura, H. / Yoshizawa, T. / Tokumoto, Y. / Suzuki, N. / Takeno, S. / Takeno, K.J. / Yamashita, T. / Tanaka, S. / Kaneko, Y. / Fujiyama, K. / Matsumura, H. / Nakazawa, Y. | |||||||||||||||
Funding support | Japan, 4items
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Citation | Journal: Commun Biol / Year: 2021 Title: Structure-function studies of ultrahigh molecular weight isoprenes provide key insights into their biosynthesis. Authors: Kajiura, H. / Yoshizawa, T. / Tokumoto, Y. / Suzuki, N. / Takeno, S. / Takeno, K.J. / Yamashita, T. / Tanaka, S.I. / Kaneko, Y. / Fujiyama, K. / Matsumura, H. / Nakazawa, Y. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bux.cif.gz | 167.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bux.ent.gz | 115 KB | Display | PDB format |
PDBx/mmJSON format | 7bux.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bux_validation.pdf.gz | 443.9 KB | Display | wwPDB validaton report |
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Full document | 7bux_full_validation.pdf.gz | 457.8 KB | Display | |
Data in XML | 7bux_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 7bux_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/7bux ftp://data.pdbj.org/pub/pdb/validation_reports/bu/7bux | HTTPS FTP |
-Related structure data
Related structure data | 7buuC 7buvC 7buwC 4kk2S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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-Components
#1: Protein | Mass: 41590.781 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eucommia ulmoides (plant) / Gene: EUFPS2, FPS2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q94IE8 #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: 2.33 Å3/Da / Density % sol: 47.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: HEPES, PEG 10000, Ethylene glycol, MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Nov 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→35.84 Å / Num. obs: 38428 / % possible obs: 98.68 % / Redundancy: 7.5 % / Biso Wilson estimate: 40.61 Å2 / CC1/2: 0.995 / Net I/σ(I): 10.77 |
Reflection shell | Resolution: 2.2→2.279 Å / Num. unique obs: 29298 / CC1/2: 0.837 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KK2 Resolution: 2.2→35.84 Å / SU ML: 0.229 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.1214 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: 57.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→35.84 Å
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Refine LS restraints |
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LS refinement shell |
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