+Open data
-Basic information
Entry | Database: PDB / ID: 6jcn | ||||||
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Title | Yeast dehydrodolichyl diphosphate synthase complex subunit NUS1 | ||||||
Components | Dehydrodolichyl diphosphate synthase complex subunit NUS1 | ||||||
Keywords | TRANSFERASE / dehydrodolichyl diphosphate synthesis / rossmann-like fold / butterfly / heterodimer / yeast RER2 / human NgBR / cis-prenyl TRANSFERASE | ||||||
Function / homology | Function and homology information Synthesis of Dolichyl-phosphate / dolichol biosynthetic process / dehydrodolichyl diphosphate synthase complex / ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] / transferase activity, transferring alkyl or aryl (other than methyl) groups / protein glycosylation / lipid droplet / nuclear envelope / nuclear membrane / membrane => GO:0016020 ...Synthesis of Dolichyl-phosphate / dolichol biosynthetic process / dehydrodolichyl diphosphate synthase complex / ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] / transferase activity, transferring alkyl or aryl (other than methyl) groups / protein glycosylation / lipid droplet / nuclear envelope / nuclear membrane / membrane => GO:0016020 / endoplasmic reticulum membrane / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 Å | ||||||
Authors | Ko, T.-P. / Ma, J. / Liu, W. / Chen, C.-C. / Guo, R.-T. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2019 Title: Structural insights to heterodimeric cis-prenyltransferases through yeast dehydrodolichyl diphosphate synthase subunit Nus1. Authors: Ma, J. / Ko, T.P. / Yu, X. / Zhang, L. / Ma, L. / Zhai, C. / Guo, R.T. / Liu, W. / Li, H. / Chen, C.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jcn.cif.gz | 192.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jcn.ent.gz | 153.3 KB | Display | PDB format |
PDBx/mmJSON format | 6jcn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/6jcn ftp://data.pdbj.org/pub/pdb/validation_reports/jc/6jcn | HTTPS FTP |
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-Related structure data
Related structure data | 5hxqS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 25861.492 Da / Num. of mol.: 2 / Mutation: C184A, C293A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: NUS1, YDL193W, D1239 / Production host: Escherichia coli (E. coli) References: UniProt: Q12063, ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.27 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M (NH4)2SO4, 0.1M Sodium Cacodylate pH 6.5, 20% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Aug 1, 2018 |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. obs: 42913 / % possible obs: 99.6 % / Redundancy: 18.8 % / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.027 / Net I/σ(I): 26.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.985 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4133 / Rpim(I) all: 0.279 / % possible all: 97.04 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HXQ Resolution: 1.998→24.837 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.33 / 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: 1.998→24.837 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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