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Yorodumi- PDB-8ylz: Structure of a cis-Geranylfarnesyl Diphosphate Synthase from Stre... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ylz | ||||||
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Title | Structure of a cis-Geranylfarnesyl Diphosphate Synthase from Streptomyces clavuligerus | ||||||
Components | Isoprenyl transferase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / cis-prenyltransferase | ||||||
Function / homology | Di-trans-poly-cis-decaprenylcistransferase-like, conserved site / Undecaprenyl pyrophosphate synthase family signature. / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily / Transferases; Transferring alkyl or aryl groups, other than methyl groups / prenyltransferase activity / magnesium ion binding / Isoprenyl transferase Function and homology information | ||||||
Biological species | Streptomyces clavuligerus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 | 8ylz.cif.gz | 60.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ylz.ent.gz | 41.3 KB | Display | PDB format |
PDBx/mmJSON format | 8ylz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/8ylz ftp://data.pdbj.org/pub/pdb/validation_reports/yl/8ylz | HTTPS FTP |
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-Related structure data
Related structure data | 8wu6C 8wu7C 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: 32477.699 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Gene: uppS2 / Organ: bacteria / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D5SL65 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.73 Å3/Da / Density % sol: 28.8 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 5.7 Details: 18% (w/v) Polyethylene glycol 4000, 0.1 M MES monohydrate (pH 5.7) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9788 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 14, 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: 1.6→34.94 Å / Num. obs: 27160 / % possible obs: 91.3 % / Redundancy: 11 % / CC1/2: 0.998 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.015 / Rrim(I) all: 0.048 / Χ2: 0.89 / Net I/σ(I): 33.2 / Num. measured all: 298879 |
Reflection shell | Resolution: 1.6→1.63 Å / % possible obs: 94.7 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.127 / Num. measured all: 12444 / Num. unique obs: 1362 / CC1/2: 0.989 / Rpim(I) all: 0.044 / Rrim(I) all: 0.135 / Χ2: 0.52 / Net I/σ(I) obs: 11.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→30.57 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.65 / 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: 1.6→30.57 Å
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Refine LS restraints |
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LS refinement shell |
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