+Open data
-Basic information
Entry | Database: PDB / ID: 5ygj | ||||||
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Title | Crystal structure of a synthase from Streptomyces sp. CL190 | ||||||
Components | Cyclolavandulyl diphosphate synthase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / substrate binding / Cyclolavandulyl diphosphate synthase / inhibitor | ||||||
Function / homology | Function and homology information plastid membrane organization / Z-farnesyl diphosphate synthase activity / dehydrodolichyl diphosphate synthase activity / polyprenyltransferase activity / polyprenol biosynthetic process / response to cold / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Streptomyces sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.648 Å | ||||||
Authors | Gao, J. / Liu, W.D. / Chen, C.C. / Guo, R.T. | ||||||
Citation | Journal: Acs Catalysis / Year: 2018 Title: Catalytic Role of Conserved Asparagine, Glutamine, Serine, and Tyrosine Residues in Isoprenoid Biosynthesis Enzymes. Authors: Malwal, S.R. / Gao, J. / Hu, X. / Yang, Y. / Liu, W. / Huang, J.W. / Ko, T.P. / Li, L. / Chen, C.C. / O'Dowd, B. / Khade, R.L. / Zhang, Y. / Zhang, Y. / Oldfield, E. / Guo, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ygj.cif.gz | 169.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ygj.ent.gz | 135 KB | Display | PDB format |
PDBx/mmJSON format | 5ygj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/5ygj ftp://data.pdbj.org/pub/pdb/validation_reports/yg/5ygj | HTTPS FTP |
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-Related structure data
Related structure data | 5ygkC 5xk3S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 24377.596 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. (strain CL190) (bacteria) Strain: CL190 / Plasmid: pET46Ek/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: X5IYJ5 #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: 2.24 Å3/Da / Density % sol: 45.03 % / Mosaicity: 0.911 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: NaAc, HEPES, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.648→25 Å / Num. obs: 24803 / % possible obs: 99.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 61.98 Å2 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.033 / Rrim(I) all: 0.063 / Χ2: 1.574 / Net I/σ(I): 17.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XK3 Resolution: 2.648→24.912 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.96 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.648→24.912 Å
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Refine LS restraints |
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LS refinement shell |
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