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Yorodumi- PDB-8wu6: Structure of a Nerylneryl Diphosphate Synthase from Solanum lycop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wu6 | ||||||
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Title | Structure of a Nerylneryl Diphosphate Synthase from Solanum lycopersicum | ||||||
Components | Nerylneryl diphosphate synthase CPT2, chloroplastic | ||||||
Keywords | BIOSYNTHETIC PROTEIN / cis-prenyltransferase | ||||||
Function / homology | Function and homology information nerylneryl diphosphate synthase / dimethylallylcistransferase activity / plastid membrane organization / dehydrodolichyl diphosphate synthase activity / polyprenol biosynthetic process / polyprenyltransferase activity / prenyltransferase activity / chloroplast stroma / response to cold / chloroplast / magnesium ion binding Similarity search - Function | ||||||
Biological species | Solanum lycopersicum (tomato) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||
Authors | Li, F.R. / Wang, Q.L. / Pan, X.M. / Dong, L.B. | ||||||
Funding support | China, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2024 Title: Discovery, Structure, and Engineering of a cis-Geranylfarnesyl Diphosphate Synthase. Authors: Li, F.R. / Wang, Q. / Pan, X. / Xu, H.M. / Dong, L.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wu6.cif.gz | 208.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wu6.ent.gz | 164.7 KB | Display | PDB format |
PDBx/mmJSON format | 8wu6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wu6_validation.pdf.gz | 442.2 KB | Display | wwPDB validaton report |
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Full document | 8wu6_full_validation.pdf.gz | 443.5 KB | Display | |
Data in XML | 8wu6_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 8wu6_validation.cif.gz | 31.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/8wu6 ftp://data.pdbj.org/pub/pdb/validation_reports/wu/8wu6 | HTTPS FTP |
-Related structure data
Related structure data | 8wu7C 8ylzC 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: 36896.305 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: CPT2 / Organ: Plant / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: K7WQ45 #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: 1.79 Å3/Da / Density % sol: 31.33 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 0.1M BICINE (pH 7.6), 30% v/v PEG monomethyl ether 550, 0.1 M Sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9788 Å |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 17, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→62.68 Å / Num. obs: 46804 / % possible obs: 99.2 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.071 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.81→1.91 Å / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 8.1 / Num. unique obs: 6864 / CC1/2: 0.98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→28.16 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.81→28.16 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 11.5374 Å / Origin y: 14.3119 Å / Origin z: 11.9537 Å
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Refinement TLS group | Selection details: all |