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- PDB-7e9s: Archaeal oligosaccharyltransferase AglB from Archaeoglobus fulgid... -

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Basic information

Entry
Database: PDB / ID: 7e9s
TitleArchaeal oligosaccharyltransferase AglB from Archaeoglobus fulgidus in complex with an inhibitory peptide and a dolichol-phosphate
Components
  • Dolichyl-phosphooligosaccharide-protein glycotransferase 3
  • a polypeptide linked to an inhibitory N-glycosylation sequon-containing peptide
KeywordsTRANSFERASE / protein n-glycosylation / ternary complex / sequon-containing peptide / dolichol-phosphate
Function / homology
Function and homology information


dolichyl-phosphooligosaccharide-protein glycotransferase / oligosaccharyl transferase activity / : / metal ion binding / plasma membrane
Similarity search - Function
Oligosaccharyl transferase, archaeal / Archaeal glycosylation protein B, peripheral domain / Archaeal glycosylation protein B long peripheral domain / : / AglB core domain / : / Oligosaccharyl transferase, STT3 subunit / Oligosaccharyl transferase STT3, N-terminal
Similarity search - Domain/homology
(2R)-2,3-DIHYDROXYPROPYL (7Z)-TETRADEC-7-ENOATE / Chem-J06 / : / DI(HYDROXYETHYL)ETHER / Dolichyl-phosphooligosaccharide-protein glycotransferase 3
Similarity search - Component
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTaguchi, Y. / Hirata, K. / Kohda, D.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP19am0101070 Japan
Japan Society for the Promotion of Science (JSPS)JP20H00405 Japan
CitationJournal: Commun Biol / Year: 2021
Title: The structure of an archaeal oligosaccharyltransferase provides insight into the strict exclusion of proline from the N-glycosylation sequon.
Authors: Taguchi, Y. / Yamasaki, T. / Ishikawa, M. / Kawasaki, Y. / Yukimura, R. / Mitani, M. / Hirata, K. / Kohda, D.
History
DepositionMar 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dolichyl-phosphooligosaccharide-protein glycotransferase 3
B: a polypeptide linked to an inhibitory N-glycosylation sequon-containing peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,93913
Polymers100,2282
Non-polymers2,71111
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-5 kcal/mol
Surface area35530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)345.740, 48.690, 63.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Dolichyl-phosphooligosaccharide-protein glycotransferase 3 / Archaeal glycosylation protein B / AglB-L / AglB-Long / Oligosaccharyl transferase / OST / OTase


Mass: 99159.875 Da / Num. of mol.: 1 / Mutation: G617C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Strain: DSM 4304 / Gene: aglB3, AF_0380 / Plasmid: pET-52b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C43
References: UniProt: O29867, dolichyl-phosphooligosaccharide-protein glycotransferase
#2: Protein/peptide a polypeptide linked to an inhibitory N-glycosylation sequon-containing peptide


Mass: 1068.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 27 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-J06 / [(3S,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34Z,39S,43S)-3,7,11,15,19,23,27,31,35,39,43,47-dodecamethyloctatetraconta-6,10,14,18,22,26,30,34-octaenyl] dihydrogen phosphate


Mass: 923.463 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C60H107O4P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-7E8 / (2R)-2,3-DIHYDROXYPROPYL (7Z)-TETRADEC-7-ENOATE / 7.7 MAG


Mass: 300.434 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H32O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY
Nonpolymer detailsWe used TMR(CARBOXYTETRAMETHYLRHODAMINE) to stand for tetramethylrhodamine (RHO), which is a ...We used TMR(CARBOXYTETRAMETHYLRHODAMINE) to stand for tetramethylrhodamine (RHO), which is a fluorescent dye. DAB: L-2,4-diaminobutyrate

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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: 2.66 Å3/Da / Density % sol: 53.84 %
Description: The microcrystals were needle-shaped with a length greater than 100 micro m and a width/thickness less than 5 micro m.
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6
Details: 50 mM NaCl, 0.1 M Na-citrate, pH 6.0, 18-22 % PEG400

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo N2 stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 20, 2019
Details: micro-focused beam of 10 micro m x 15 micro m (horizontal x vertical)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→49.4 Å / Num. obs: 30677 / % possible obs: 100 % / Redundancy: 79.5 % / Biso Wilson estimate: 70.16 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.432 / Rrim(I) all: 0.435 / Net I/σ(I): 13.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 76.9 % / Rmerge(I) obs: 8.718 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3054 / CC1/2: 0.756 / Rrim(I) all: 8.776 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
PHENIX1.18.2_3874refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GMY

5gmy


Resolution: 2.7→24.84 Å / SU ML: 0.3262 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.7132
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2522 1485 4.85 %
Rwork0.2152 29115 -
obs0.2171 30599 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79 Å2
Refinement stepCycle: LAST / Resolution: 2.7→24.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7032 0 185 16 7233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00287434
X-RAY DIFFRACTIONf_angle_d0.591610097
X-RAY DIFFRACTIONf_chiral_restr0.04751081
X-RAY DIFFRACTIONf_plane_restr0.00471253
X-RAY DIFFRACTIONf_dihedral_angle_d17.44231072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.790.36581300.32556X-RAY DIFFRACTION99.67
2.79-2.890.32581310.27012628X-RAY DIFFRACTION99.86
2.89-30.30041390.26292549X-RAY DIFFRACTION100
3-3.140.29521100.25712621X-RAY DIFFRACTION100
3.14-3.30.32761360.23622622X-RAY DIFFRACTION100
3.3-3.510.25971320.22912649X-RAY DIFFRACTION99.89
3.51-3.780.25971330.20422635X-RAY DIFFRACTION100
3.78-4.160.20461260.1932638X-RAY DIFFRACTION100
4.16-4.760.19651300.18162674X-RAY DIFFRACTION100
4.76-5.980.26221530.21822695X-RAY DIFFRACTION99.93
5.98-24.840.24791650.21112848X-RAY DIFFRACTION99.87
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.65642887792-0.16818662171-0.4634246923821.02911265157-0.2288386417831.36192220352-0.08868684347440.178383943979-0.18820874235-0.1368386882440.0890878253578-0.07309024053490.1991324239560.024577166164-0.0004738714742840.423150552669-0.00709252777927-0.01306665667390.401234478178-0.08457154908950.485971559163-28.30995422947.0834378984916.336543526
20.8768067173-0.1143184607470.37391318040.593071506850.4330459910931.82071941083-0.0237812793045-0.0812156293144-0.1444418605980.06988393952340.1238221746910.06551464643080.21672085075-0.0522357349663-0.09209033230260.453387125495-0.02779610724960.01090877792740.4167291087650.05910709559440.642646313386-72.932446882410.066675080914.2598377012
35.163496012514.963454861154.11451653267.897931168686.43173703176.36365130358-2.133086783733.614727588622.65678712874-2.186246784580.1265949921692.15205772586-1.37651335364-0.3789847747112.016082283040.898191003185-0.0228573789378-0.1345703956581.547731505140.1240998525341.12073400939-52.07375231177.872485434569.6435436949
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 6 through 492 )AA6 - 4921 - 487
22chain 'A' and (resid 493 through 872 )AA493 - 872488 - 867
33chain 'B' and (resid 1 through 9 )BC1 - 91 - 9

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