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- PDB-6w2l: Crystal structure of human dehydrodolichyl diphosphate synthase (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6w2l | |||||||||
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Title | Crystal structure of human dehydrodolichyl diphosphate synthase (NgBR/DHDDS) in complex with Mg and IPP | |||||||||
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Function / homology | ![]() protein mannosylation / Defective DHDDS causes RP59 / dolichol biosynthetic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Edani, B.H. / Ha, Y. / Sessa, W.C. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural elucidation of thecis-prenyltransferase NgBR/DHDDS complex reveals insights in regulation of protein glycosylation. Authors: Edani, B.H. / Grabinska, K.A. / Zhang, R. / Park, E.J. / Siciliano, B. / Surmacz, L. / Ha, Y. / Sessa, W.C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.3 KB | Display | ![]() |
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PDB format | ![]() | 88.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 38455.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Details (production host): Bacterial expression, coexpression Production host: ![]() ![]() ![]() References: UniProt: Q86SQ9, ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] | ||||
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#2: Protein | ![]() Mass: 24086.416 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Details (production host): Bacterial expression, coexpression Production host: ![]() ![]() ![]() References: UniProt: Q96E22, ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] | ||||
#3: Chemical | ChemComp-MG / | ||||
#4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.21 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 2.5 mM MgCl2, 3.3 mM IPP, 0.1 M Bicine, 10% v/v 2-propanol, 22% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.306→40 Å / Num. obs: 31367 / % possible obs: 99.2 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.032 / Rrim(I) all: 0.113 / Χ2: 1.001 / Net I/av σ(I): 29.6 / Net I/σ(I): 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1X06, 6JCN Resolution: 2.306→37.916 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 11.973 / SU ML: 0.262 / Cross valid method: FREE R-VALUE / ESU R: 0.276 / ESU R Free: 0.224 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.717 Å2
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Refinement step | Cycle: LAST / Resolution: 2.306→37.916 Å
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Refine LS restraints |
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LS refinement shell |
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