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- PDB-5gmy: Crystal structure of the Archaeoglobus fulgidus oligosaccharyltra... -

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Basic information

Entry
Database: PDB / ID: 5gmy
TitleCrystal structure of the Archaeoglobus fulgidus oligosaccharyltransferase (O29867_ARCFU) tethered with an acceptor peptide containing the NVT sequon via a disulfide bond
Components
  • Transmembrane oligosaccharyl transferase, putative
  • acceptor peptide, ARG-TYR-ASN-VAL-THR-ALA-CYS
KeywordsTRANSFERASE / Oligosaccharyltransferase / N-lineked glycosylation / AglB / Archaeoglobus fulgidus
Function / homology
Function and homology information


dolichyl-phosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / post-translational protein modification / metal ion binding / plasma membrane
Similarity search - Function
Immunoglobulin-like - #3390 / Oligosaccharyl transferase, archaeal / Archaeal glycosylation protein B, peripheral domain / Archaeal glycosylation protein B long peripheral domain / : / Oligosaccharyl transferase, STT3 subunit / Oligosaccharyl transferase STT3, N-terminal / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Dolichyl-phosphooligosaccharide-protein glycotransferase 3
Similarity search - Component
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsMatsumoto, S. / Kohda, D.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP24370047, JP26119002 Japan
CitationJournal: Biochemistry / Year: 2017
Title: Tethering an N-Glycosylation Sequon-Containing Peptide Creates a Catalytically Competent Oligosaccharyltransferase Complex
Authors: Matsumoto, S. / Taguchi, Y. / Shimada, A. / Igura, M. / Kohda, D.
History
DepositionJul 18, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Mar 31, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / audit_author / cell / citation_author / diffrn / pdbx_audit_support / pdbx_entity_src_syn / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct_conf / struct_conn / struct_conn_type / struct_mon_prot_cis / struct_ref_seq / struct_sheet_range / struct_site / struct_site_gen / symmetry
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _audit_author.identifier_ORCID / _cell.volume / _citation_author.identifier_ORCID / _diffrn.pdbx_serial_crystal_experiment / _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _reflns_shell.number_unique_obs / _software.version / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _symmetry.space_group_name_Hall
Description: Ligand geometry
Details: We moved the position of the bound Mg2+ ion to a proper place and refined the whole structure again. This is an important correction because this metal ion is located at the center of the catalytic site.
Provider: author / Type: Coordinate replacement
Revision 2.1Nov 8, 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: Transmembrane oligosaccharyl transferase, putative
B: acceptor peptide, ARG-TYR-ASN-VAL-THR-ALA-CYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0113
Polymers99,9872
Non-polymers241
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-16 kcal/mol
Surface area34450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.549, 121.549, 181.344
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw

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Components

#1: Protein Transmembrane oligosaccharyl transferase, putative / Oligosaccharyltransferase


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: AF_0380 / Production host: Escherichia coli (E. coli)
References: UniProt: O29867, dolichyl-diphosphooligosaccharide-protein glycotransferase
#2: Protein/peptide acceptor peptide, ARG-TYR-ASN-VAL-THR-ALA-CYS


Mass: 826.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN

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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: 3.35 Å3/Da / Density % sol: 63.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10 mM MgCl2, 0.1 M Bis-Tris, pH 6.5, 22 % (w/v) PEG 550MME, 5% (v/v) Jeffamine M-600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.5→49.9 Å / Num. obs: 17649 / % possible obs: 99.8 % / Redundancy: 13.9 % / Biso Wilson estimate: 147.08 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 44.7
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 14.2 % / Rmerge(I) obs: 1.283 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 828 / CC1/2: 0.956 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WAK

3wak


Resolution: 3.5→40.1 Å / SU ML: 0.5571 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.3813
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.274 886 5.08 %
Rwork0.226 16567 -
obs0.2282 17453 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 202.48 Å2
Refinement stepCycle: LAST / Resolution: 3.5→40.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6886 0 1 0 6887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00237111
X-RAY DIFFRACTIONf_angle_d0.56149702
X-RAY DIFFRACTIONf_chiral_restr0.04231046
X-RAY DIFFRACTIONf_plane_restr0.0041209
X-RAY DIFFRACTIONf_dihedral_angle_d9.3373948
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.720.44191690.37132616X-RAY DIFFRACTION96.57
3.72-4.010.3231560.29232718X-RAY DIFFRACTION99.34
4.01-4.410.30181570.24252735X-RAY DIFFRACTION99.52
4.41-5.050.26621480.22512788X-RAY DIFFRACTION99.69
5.05-6.360.31331340.25752824X-RAY DIFFRACTION99.76
6.36-40.10.21871220.18512886X-RAY DIFFRACTION95.89
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)
10.964323749732-0.382800122046-0.3754340980941.38250959435-1.421763034712.09490219172-0.171491875880.3778324952340.0634408754747-0.452068161722-0.0030297663579-0.030664714790.506846411302-0.4003688879790.2322738999951.68078308649-0.3175337685230.08350989014441.78531691464-0.07178685425021.522610485730.3275535123-51.581354965620.5002449482
21.893189281360.5669391043130.1102239857051.27595917593-0.5556801853362.56780750264-0.1750561788980.7337625365040.651174132842-0.0831653962846-0.0442579592152-0.354406722639-0.2490508389050.4421964055050.328571876541.71149382199-0.0253470018081-0.1779952614082.211250895270.368532445642.1562712528232.7579196344-10.69901684013.99305394034
31.54246550217-0.3030761729393.217456428870.0636879850352-0.6524714696336.74821300265-0.0222165172603-0.315526055762-0.4922202688490.998498417623-0.1834153211030.660455822640.374249166848-0.3255733033450.2663032486712.02696084521-0.631574779586-0.3453838505941.61582575690.4341679243912.6388512998734.2928834216-30.515210945716.1795136674
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 5 through 533 )AA5 - 5331 - 513
22chain 'A' and (resid 534 through 868 )AA534 - 868514 - 848
33chain 'B' and (resid 1 through 7 )BB1 - 71 - 7

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