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- PDB-6jcn: Yeast dehydrodolichyl diphosphate synthase complex subunit NUS1 -

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Basic information

Entry
Database: PDB / ID: 6jcn
TitleYeast dehydrodolichyl diphosphate synthase complex subunit NUS1
ComponentsDehydrodolichyl diphosphate synthase complex subunit NUS1
KeywordsTRANSFERASE / 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
Dehydrodolichyl diphosphate synthase complex subunit Nus1 / Decaprenyl diphosphate synthase-like superfamily
Similarity search - Domain/homology
Dehydrodolichyl diphosphate synthase complex subunit NUS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 Å
AuthorsKo, T.-P. / Ma, J. / Liu, W. / Chen, C.-C. / Guo, R.-T.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-KPQ-105-TPP Taiwan
CitationJournal: 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
DepositionJan 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dehydrodolichyl diphosphate synthase complex subunit NUS1
B: Dehydrodolichyl diphosphate synthase complex subunit NUS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9154
Polymers51,7232
Non-polymers1922
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-56 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.328, 82.671, 131.835
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dehydrodolichyl diphosphate synthase complex subunit NUS1 / / Nuclear undecaprenyl pyrophosphate synthase 1


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 ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 461 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.27 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 1, 2018
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.1802 1999 4.67 %
Rwork0.1524 --
obs0.1537 42840 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.998→24.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3274 0 10 461 3745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083407
X-RAY DIFFRACTIONf_angle_d0.9374620
X-RAY DIFFRACTIONf_dihedral_angle_d13.7372042
X-RAY DIFFRACTIONf_chiral_restr0.06515
X-RAY DIFFRACTIONf_plane_restr0.007586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9981-2.0480.26651290.2592637X-RAY DIFFRACTION90
2.048-2.10340.24911380.22562818X-RAY DIFFRACTION98
2.1034-2.16520.26151410.20482874X-RAY DIFFRACTION99
2.1652-2.23510.24481430.17822913X-RAY DIFFRACTION100
2.2351-2.31490.20971420.17132908X-RAY DIFFRACTION100
2.3149-2.40750.20891420.16642911X-RAY DIFFRACTION100
2.4075-2.5170.21581430.16822931X-RAY DIFFRACTION100
2.517-2.64950.19891430.16282921X-RAY DIFFRACTION100
2.6495-2.81530.19631430.15872920X-RAY DIFFRACTION100
2.8153-3.03240.20711440.1712929X-RAY DIFFRACTION100
3.0324-3.33690.18391450.15532966X-RAY DIFFRACTION100
3.3369-3.81820.1711450.13332969X-RAY DIFFRACTION100
3.8182-4.80490.12321470.11593014X-RAY DIFFRACTION100
4.8049-24.83850.16641540.14983130X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.475-0.02151.18411.69180.64662.10340.0371-0.23150.16650.3556-0.13140.0007-0.1205-0.247-00.3905-0.03890.0030.2985-0.03170.271317.91935.861188.2618
21.78160.49920.66462.34030.12242.3834-0.06740.06330.1428-0.0857-0.12060.0887-0.458-0.3274-0.02650.36780.0289-0.03970.2586-0.01970.276815.862543.501780.421
31.5681-2.1042-1.14830.66261.35272.39940.2710.09440.3039-0.2571-0.142-0.1587-0.52190.12110.03550.3219-0.0170.03690.30940.02450.337828.399732.175765.6382
41.2983-0.6257-1.07361.80610.61912.1491-0.0156-0.1720.14910.3387-0.0278-0.04430.2980.2527-0.00880.3775-0.0252-0.03090.2759-0.00790.279526.74528.443989.188
50.9389-1.339-0.69211.9697-0.31132.0884-0.2863-0.12940.10880.12040.1133-0.12870.28390.4533-0.00130.2618-0.0049-0.02230.35130.01780.315740.08498.296389.5083
61.782-0.0978-0.40412.70380.51712.1983-0.11590.0801-0.1036-0.1399-0.0841-0.17530.47980.5584-0.0970.28830.09430.04130.37640.05350.290843.7810.887382.074
70.96-1.15520.65530.7683-0.58183.31520.18520.108-0.2751-0.1834-0.24020.17530.32370.14420.00820.22930.0248-0.04940.2805-0.03270.308232.056911.280465.8712
81.0652-0.57921.13462.1342-0.71422.2231-0.161-0.2616-0.04610.35420.04610.1349-0.3759-0.4117-0.00320.31210.01230.02450.317-0.0110.318430.444114.697689.4476
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 151 through 191 )
2X-RAY DIFFRACTION2chain 'A' and (resid 192 through 248 )
3X-RAY DIFFRACTION3chain 'A' and (resid 262 through 317 )
4X-RAY DIFFRACTION4chain 'A' and (resid 318 through 370 )
5X-RAY DIFFRACTION5chain 'B' and (resid 151 through 191 )
6X-RAY DIFFRACTION6chain 'B' and (resid 192 through 248 )
7X-RAY DIFFRACTION7chain 'B' and (resid 262 through 317 )
8X-RAY DIFFRACTION8chain 'B' and (resid 318 through 370 )

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