PDB-5ogl: Structure of bacterial oligosaccharyltransferase PglB in complex ...

ID or keywords:

Entry

Database: PDB / ID: 5ogl

Title

Structure of bacterial oligosaccharyltransferase PglB in complex with an acceptor peptide and an lipid-linked oligosaccharide analog

Components

Substrate mimicking peptide
Undecaprenyl-diphosphooligosaccharide--protein glycotransferase

Keywords

MEMBRANE PROTEIN /

Oligosaccharyltransferase /

Complex / Protein N-glycosylation /

Bacteria

Function / homology

Function and homology information

undecaprenyl-diphosphooligosaccharide-protein glycotransferase /

oligosaccharyl transferase activity / protein N-linked glycosylation via asparagine /

glycosyltransferase activity / magnesium ion binding /

plasma membrane
Similarity search - Function

Biological species

Campylobacter lari (Campylobacter)

Campylobacter jejuni (Campylobacter)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Napiorkowska, M. / Boilevin, J. / Sovdat, T. / Darbre, T. / Reymond, J.-L. / Aebi, M. / Locher, K.P.

Citation

Journal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Molecular basis of lipid-linked oligosaccharide recognition and processing by bacterial oligosaccharyltransferase.
Authors: Napiorkowska, M. / Boilevin, J. / Sovdat, T. / Darbre, T. / Reymond, J.L. / Aebi, M. / Locher, K.P.

History

Deposition	Jul 13, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 25, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 1, 2017	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2	Dec 20, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Jan 17, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_conn_type.id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ogl.cif.gz	310.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5ogl.ent.gz	254.9 KB	Display	PDB format
PDBx/mmJSON format	5ogl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/og/5ogl ftp://data.pdbj.org/pub/pdb/validation_reports/og/5ogl	HTTPS FTP

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Related structure data

Related structure data	3rceS S: Starting model for refinement
Similar structure data	5fl1-1 2ztg-d 4n43-d 3iyc-d 5mi7-d 5abg-1 6iy9-d 2xm2-1 3ju8-d 6lhb-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#266 - Feb 2022 Oligosaccharyltransferase similarity (9)

Deposited unit

A: Undecaprenyl-diphosphooligosaccharide--protein glycotransferase

B: Substrate mimicking peptide

hetero molecules

84.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	83.940, 116.180, 172.020
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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

#1: Protein	Undecaprenyl-diphosphooligosaccharide--protein glycotransferase / Protein glycosylation B Mass: 83037.312 Da / Num. of mol.: 1 Mutation: K2E, C17A, C30A, A108T, C360L, N535Q, Q536K, K549P, D550N, F553I, N556P, A600P, A602D, T606K, T607Q, V610I, M611T, I619S, F622Y, A624S, V627I, A630N, F663Y, F670Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter lari (strain RM2100 / D67 / ATCC BAA-1060) (Campylobacter) Strain: RM2100 / D67 / ATCC BAA-1060 / Gene: pglB, Cla_1253 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: B9KDD4, undecaprenyl-diphosphooligosaccharide-protein glycotransferase
#2: Protein/peptide	Substrate mimicking peptide Mass: 853.792 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Campylobacter jejuni (Campylobacter)

#1: Protein

Undecaprenyl-diphosphooligosaccharide--protein glycotransferase / Protein glycosylation B

Mass: 83037.312 Da / Num. of mol.: 1
Mutation: K2E, C17A, C30A, A108T, C360L, N535Q, Q536K, K549P, D550N, F553I, N556P, A600P, A602D, T606K, T607Q, V610I, M611T, I619S, F622Y, A624S, V627I, A630N, F663Y, F670Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Campylobacter lari (strain RM2100 / D67 / ATCC BAA-1060) (Campylobacter)
Strain: RM2100 / D67 / ATCC BAA-1060 / Gene: pglB, Cla_1253 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B9KDD4,

undecaprenyl-diphosphooligosaccharide-protein glycotransferase

#2: Protein/peptide

Substrate mimicking peptide

Mass: 853.792 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.)

Campylobacter jejuni (Campylobacter)

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Non-polymers , 4 types, 24 molecules

#3: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical	ChemComp-9UB / [(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]methyl-[oxidanyl-[(2~{Z},6~{Z},10~{Z})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenoxy]phosphoryl]oxy-phosphinic acid Mass: 651.663 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₉H₅₁NO₁₁P₂
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 5 Å³/Da / Density % sol: 75.4 %
Crystal grow	Temperature: 293 K / Method: evaporation / pH: 9.4 Details: 0.1M glycine pH 9.4, 0.12M lithium sulfate, 29-31% PEG400

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.7→47.767 Å / Num. obs: 46914 / % possible obs: 100 % / Redundancy: 12.8 % / R_merge(I) obs: 0.08725 / R_rim(I) all: 0.09107 / Net I/σ(I): 21.5
Reflection shell	Resolution: 2.7→2.8 Å / Redundancy: 13.5 % / R_merge(I) obs: 1.358 / Mean I/σ(I) obs: 2.18 / Num. unique all: 4593 / CC_1/2: 0.78 / % possible all: 100

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Processing

Software

Name	Classification
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3RCE

3rce

Resolution: 2.7→47.767 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 25.32

	R_factor	Num. reflection	% reflection
R_free	0.2439	4481	5.03 %
R_work	0.2171	-	-
obs	0.2185	46899	99.93 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.7→47.767 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5875	0	46	20	5941

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	6072
X-RAY DIFFRACTION	f_angle_d	1.117	8233
X-RAY DIFFRACTION	f_dihedral_angle_d	14.931	3545
X-RAY DIFFRACTION	f_chiral_restr	0.06	917
X-RAY DIFFRACTION	f_plane_restr	0.006	1012

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.6999-2.7305	0.4014	145	0.3681	2748	X-RAY DIFFRACTION	100
2.7305-2.7626	0.419	152	0.3695	2855	X-RAY DIFFRACTION	100
2.7626-2.7963	0.3913	149	0.3581	2801	X-RAY DIFFRACTION	100
2.7963-2.8317	0.3491	150	0.3189	2806	X-RAY DIFFRACTION	100
2.8317-2.869	0.3163	152	0.2958	2831	X-RAY DIFFRACTION	100
2.869-2.9083	0.4001	149	0.2922	2860	X-RAY DIFFRACTION	100
2.9083-2.9498	0.3666	148	0.305	2781	X-RAY DIFFRACTION	100
2.9498-2.9938	0.3507	155	0.2816	2865	X-RAY DIFFRACTION	100
2.9938-3.0406	0.2621	148	0.2647	2815	X-RAY DIFFRACTION	100
3.0406-3.0905	0.3216	149	0.2763	2813	X-RAY DIFFRACTION	100
3.0905-3.1437	0.332	150	0.2623	2817	X-RAY DIFFRACTION	100
3.1437-3.2009	0.3028	150	0.2636	2819	X-RAY DIFFRACTION	100
3.2009-3.2624	0.2599	146	0.2482	2815	X-RAY DIFFRACTION	100
3.2624-3.329	0.247	153	0.2453	2844	X-RAY DIFFRACTION	100
3.329-3.4014	0.3185	151	0.2589	2813	X-RAY DIFFRACTION	100
3.4014-3.4805	0.2427	149	0.2114	2837	X-RAY DIFFRACTION	100
3.4805-3.5675	0.2141	146	0.2109	2778	X-RAY DIFFRACTION	100
3.5675-3.6639	0.2481	154	0.2076	2881	X-RAY DIFFRACTION	100
3.6639-3.7717	0.2422	148	0.2029	2804	X-RAY DIFFRACTION	100
3.7717-3.8934	0.2356	152	0.1972	2800	X-RAY DIFFRACTION	100
3.8934-4.0325	0.1859	149	0.1905	2851	X-RAY DIFFRACTION	100
4.0325-4.1938	0.2518	149	0.1934	2821	X-RAY DIFFRACTION	100
4.1938-4.3846	0.2114	148	0.1853	2828	X-RAY DIFFRACTION	100
4.3846-4.6156	0.2197	152	0.1867	2828	X-RAY DIFFRACTION	100
4.6156-4.9045	0.206	148	0.1736	2818	X-RAY DIFFRACTION	100
4.9045-5.2827	0.198	144	0.173	2835	X-RAY DIFFRACTION	100
5.2827-5.8135	0.2039	150	0.1982	2819	X-RAY DIFFRACTION	100
5.8135-6.6528	0.2157	151	0.2099	2821	X-RAY DIFFRACTION	100
6.6528-8.3745	0.2239	152	0.2055	2841	X-RAY DIFFRACTION	100
8.3745-47.7745	0.2635	142	0.2402	2798	X-RAY DIFFRACTION	99

Refinement TLS params.

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

ID	L11 (°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)
1	1.3347	-0.1149	0.1624	1.5138	0.4455	2.7932	0.0687	0.0765	-0.0621	0.1752	0.015	0.0334	-0.1282	0.1473	-0.0775	0.3821	-0.034	0.0595	0.4153	-0.0366	0.5566	92.3862	35.3888	190.8281
2	7.3868	-0.1491	4.4639	4.4829	-0.2866	9.0056	-0.1352	-1.1177	0.5058	1.3566	0.3564	0.2939	-1.4223	-0.8653	-0.147	1.1436	0.0602	0.2268	0.6861	-0.1244	1.0319	83.7097	61.2368	215.7109
3	5.5889	2.0088	-2.3755	2.6588	-2.804	2.9155	0.1064	-0.6214	0.8583	0.4246	0.0306	0.2522	-1.7323	-0.2794	-0.0623	1.4331	0.0387	-0.149	1.1729	-0.1178	1.3665	72.048	44.9204	182.5519
4	6.1489	1.1686	-0.6761	3.9584	-4.4223	5.0617	0.2026	-0.6834	-0.5399	0.705	-0.1412	-0.2947	1.1205	0.1455	0.0553	1.5002	0.014	-0.0389	0.7245	-0.0179	0.8052	93.4685	14.0307	225.3915
5	8.9776	5.0767	-4.0402	6.1596	-0.9313	7.7521	0.4813	1.4397	1.966	-0.9429	-0.2715	0.9445	-1.3385	-0.1431	-0.2781	1.173	0.1302	-0.1661	0.7665	0.1775	1.1958	80.3287	49.9258	160.2624
6	8.8126	2.3958	3.9348	5.975	3.0508	6.3469	0.6896	0.2874	-2.6716	0.282	0.1424	-0.2671	2.0887	0.8509	-0.662	1.0284	0.1093	-0.1219	0.7686	-0.0734	1.3269	85.8666	7.7574	167.758
7	8.0811	6.4758	3.7644	5.5801	4.4347	7.3171	-0.1475	-0.9189	-0.3125	-0.1953	-0.3118	0.6718	-0.6188	-0.2132	0.4421	0.6866	-0.0463	0.1149	0.5664	-0.0824	0.6579	88.2386	30.0744	185.6597
8	0.0415	0.0107	-0.0353	0.0043	-0.0104	0.0349	-0.0109	0.0609	0.0422	-0.0591	0.0514	-0.051	-0.0325	-0.0135	0.0001	0.9957	-0.1144	0.1063	0.7398	-0.1541	1.0577	84.5313	41.6961	194.9064

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and ((resseq 2:237) or (resseq 282:293) or (resseq 310:395) or (resseq 423:528) or (resseq 559:598) or (resseq 635:711))
2	X-RAY DIFFRACTION	2	chain 'A' and ((resseq 238:281))
3	X-RAY DIFFRACTION	3	chain 'A' and ((resseq 294:309))
4	X-RAY DIFFRACTION	4	chain 'A' and ((resseq 396:422))
5	X-RAY DIFFRACTION	5	chain 'A' and ((resseq 529:558))
6	X-RAY DIFFRACTION	6	chain 'A' and ((resseq 599:634))
7	X-RAY DIFFRACTION	7	chain 'B'
8	X-RAY DIFFRACTION	8	chain 'Q'

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