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- PDB-3g7y: Crystal structure of oxidized Ost6L -

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Basic information

Entry
Database: PDB / ID: 3g7y
TitleCrystal structure of oxidized Ost6L
ComponentsDolichyl-diphosphooligosaccharide-protein glycosyltransferase subunit OST6
KeywordsTRANSFERASE / OXIDOREDUCTASE / ACTIVE SITE LOOP / REDOX STATE / Membrane / Transmembrane
Function / homology
Function and homology information


Miscellaneous transport and binding events / oligosaccharyltransferase complex / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / protein-disulfide reductase activity / Neutrophil degranulation / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Oligosaccharyl transferase complex, subunit OST3/OST6 / OST3 / OST6 family, transporter family / Glutaredoxin / Glutaredoxin / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.215 Å
AuthorsStirnimann, C.U. / Grimshaw, J.P.A. / Schulz, B.L. / Brozzo, M.S. / Fritsch, F. / Glockshuber, R. / Capitani, G. / Gruetter, M.G. / Aebi, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Oxidoreductase activity of oligosaccharyltransferase subunits Ost3p and Ost6p defines site-specific glycosylation efficiency.
Authors: Schulz, B.L. / Stirnimann, C.U. / Grimshaw, J.P. / Brozzo, M.S. / Fritsch, F. / Mohorko, E. / Capitani, G. / Glockshuber, R. / Grutter, M.G. / Aebi, M.
History
DepositionFeb 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 3, 2024Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dolichyl-diphosphooligosaccharide-protein glycosyltransferase subunit OST6


Theoretical massNumber of molelcules
Total (without water)20,3431
Polymers20,3431
Non-polymers00
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.031, 59.391, 105.866
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Dolichyl-diphosphooligosaccharide-protein glycosyltransferase subunit OST6 / Oligosaccharyl transferase subunit OST6 / Oligosaccharyl transferase 37 kDa subunit / OTase 37 kDa subunit


Mass: 20342.777 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: OST6, YML019W / Plasmid: pBAD-ost6L-His10 / Production host: Escherichia coli (E. coli) / Strain (production host): Top 10 / References: UniProt: Q03723, EC: 2.4.1.119
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 18% PEG 3350, 50 mM Na-citrate, pH 3.0, protein solution buffer: 50 mM Tris-HCl, pH 8.0 mixing ratio 1.5(protein):1(precipitant), VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 5, 2007
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.21→22.31 Å / Num. obs: 9389 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 27.9 Å2 / Rsym value: 0.087 / Net I/σ(I): 18
Reflection shellResolution: 2.21→2.3 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 5.9 / Rsym value: 0.329 / % possible all: 92

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHELXEmodel building
autoSHARPphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: Ost6L structure solved by SAD (bromide signal)

Resolution: 2.215→22.31 Å / SU ML: 0.36 / Isotropic thermal model: ISOTROPIC / σ(F): 1.4 / Phase error: 26.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2796 1160 12.36 %
Rwork0.2186 --
obs0.2258 9387 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.263 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 30.6 Å2
Baniso -1Baniso -2Baniso -3
1--5.7556 Å20 Å20 Å2
2--11.7288 Å20 Å2
3----5.9732 Å2
Refinement stepCycle: LAST / Resolution: 2.215→22.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1219 0 0 77 1296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051250
X-RAY DIFFRACTIONf_angle_d0.9081706
X-RAY DIFFRACTIONf_dihedral_angle_d18.382447
X-RAY DIFFRACTIONf_chiral_restr0.059195
X-RAY DIFFRACTIONf_plane_restr0.004223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.215-2.3160.35581450.3235990X-RAY DIFFRACTION98
2.316-2.4380.33281480.2582991X-RAY DIFFRACTION100
2.438-2.59050.27551550.22621016X-RAY DIFFRACTION100
2.5905-2.79020.27551640.2203995X-RAY DIFFRACTION100
2.7902-3.07030.36121330.21851033X-RAY DIFFRACTION100
3.0703-3.51310.2141330.21021038X-RAY DIFFRACTION100
3.5131-4.42050.24051380.17881052X-RAY DIFFRACTION100
4.4205-22.31690.25811440.20231112X-RAY DIFFRACTION100

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