PDB-6o1j: Alpha-L-fucosidase AlfC fucosyltransferase mutant N243A

ID or keywords:

Entry

Database: PDB / ID: 6o1j

Title

Alpha-L-fucosidase AlfC fucosyltransferase mutant N243A

Components

AlfC

Keywords

HYDROLASE /

Fucosidase /

fucosyltransferase / AlfC

Function / homology

Function and homology information

alpha-L-fucosidase activity / fucose metabolic process
Similarity search - Function

Biological species

Lactobacillus casei (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2 Å

Authors

Klontz, E.H. / Sundberg, E.J.

Citation

Journal: Nat Commun / Year: 2020
Title: Structure and dynamics of an alpha-fucosidase reveal a mechanism for highly efficient IgG transfucosylation.
Authors: Klontz, E.H. / Li, C. / Kihn, K. / Fields, J.K. / Beckett, D. / Snyder, G.A. / Wintrode, P.L. / Deredge, D. / Wang, L.X. / Sundberg, E.J.

History

Deposition	Feb 20, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 26, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2	Dec 16, 2020	Group: Database references / Structure summary / Category: chem_comp / citation / citation_author Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3	Oct 11, 2023	Group: 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_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6o1j.cif.gz	1 MB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o1/6o1j ftp://data.pdbj.org/pub/pdb/validation_reports/o1/6o1j	HTTPS FTP

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Related structure data

Related structure data	6o18SC 6o1aC 6o1cC 6o1iC 6oheC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6o18-1 6o1a-2 6ohe-2 6o1a-1 6o1i-1 6o1c-2 6o18-2 6o1i-2 6ohe-1 6o1c-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

6o18SC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: AlfC

B: AlfC

C: AlfC

D: AlfC

E: AlfC

F: AlfC

G: AlfC

H: AlfC

hetero molecules

316 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: AlfC

C: AlfC

E: AlfC

G: AlfC

hetero molecules

defined by author
Evidence: gel filtration, AlfC forms a tetramer, based off of gel filtration, native mass spectrometry, and analytical ultracentrifugation.
158 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: AlfC

H: AlfC

hetero molecules

D: AlfC

F: AlfC

hetero molecules

defined by author
158 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

D: AlfC

F: AlfC

hetero molecules

B: AlfC

H: AlfC

hetero molecules

defined by author
158 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	80.301, 259.921, 80.350
Angle α, β, γ (deg.)	90.000, 118.810, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MET	MET	LEU	LEU	A	A	1 - 345	1 - 345
2	1	MET	MET	LEU	LEU	B	B	1 - 345	1 - 345
1	2	ASN	ASN	LEU	LEU	A	A	2 - 345	2 - 345
2	2	ASN	ASN	LEU	LEU	C	C	2 - 345	2 - 345
1	3	MET	MET	LEU	LEU	A	A	1 - 345	1 - 345
2	3	MET	MET	LEU	LEU	D	D	1 - 345	1 - 345
1	4	ASN	ASN	LEU	LEU	A	A	2 - 345	2 - 345
2	4	ASN	ASN	LEU	LEU	E	E	2 - 345	2 - 345
1	5	MET	MET	LEU	LEU	A	A	1 - 345	1 - 345
2	5	MET	MET	LEU	LEU	F	F	1 - 345	1 - 345
1	6	ASN	ASN	LEU	LEU	A	A	4 - 345	4 - 345
2	6	ASN	ASN	LEU	LEU	G	G	4 - 345	4 - 345
1	7	MET	MET	LEU	LEU	A	A	1 - 345	1 - 345
2	7	MET	MET	LEU	LEU	H	H	1 - 345	1 - 345
1	8	ASN	ASN	ARG	ARG	B	B	2 - 344	2 - 344
2	8	ASN	ASN	ARG	ARG	C	C	2 - 344	2 - 344
1	9	MET	MET	LEU	LEU	B	B	1 - 345	1 - 345
2	9	MET	MET	LEU	LEU	D	D	1 - 345	1 - 345
1	10	ASN	ASN	LEU	LEU	B	B	2 - 345	2 - 345
2	10	ASN	ASN	LEU	LEU	E	E	2 - 345	2 - 345
1	11	MET	MET	LEU	LEU	B	B	1 - 345	1 - 345
2	11	MET	MET	LEU	LEU	F	F	1 - 345	1 - 345
1	12	ASN	ASN	LEU	LEU	B	B	4 - 345	4 - 345
2	12	ASN	ASN	LEU	LEU	G	G	4 - 345	4 - 345
1	13	MET	MET	LEU	LEU	B	B	1 - 345	1 - 345
2	13	MET	MET	LEU	LEU	H	H	1 - 345	1 - 345
1	14	ASN	ASN	LEU	LEU	C	C	2 - 345	2 - 345
2	14	ASN	ASN	LEU	LEU	D	D	2 - 345	2 - 345
1	15	ASN	ASN	LEU	LEU	C	C	2 - 345	2 - 345
2	15	ASN	ASN	LEU	LEU	E	E	2 - 345	2 - 345
1	16	ASN	ASN	LEU	LEU	C	C	2 - 345	2 - 345
2	16	ASN	ASN	LEU	LEU	F	F	2 - 345	2 - 345
1	17	ASN	ASN	LEU	LEU	C	C	4 - 345	4 - 345
2	17	ASN	ASN	LEU	LEU	G	G	4 - 345	4 - 345
1	18	ASN	ASN	LEU	LEU	C	C	2 - 345	2 - 345
2	18	ASN	ASN	LEU	LEU	H	H	2 - 345	2 - 345
1	19	ASN	ASN	LEU	LEU	D	D	2 - 345	2 - 345
2	19	ASN	ASN	LEU	LEU	E	E	2 - 345	2 - 345
1	20	MET	MET	LEU	LEU	D	D	1 - 345	1 - 345
2	20	MET	MET	LEU	LEU	F	F	1 - 345	1 - 345
1	21	ASN	ASN	LEU	LEU	D	D	4 - 345	4 - 345
2	21	ASN	ASN	LEU	LEU	G	G	4 - 345	4 - 345
1	22	MET	MET	LEU	LEU	D	D	1 - 345	1 - 345
2	22	MET	MET	LEU	LEU	H	H	1 - 345	1 - 345
1	23	ASN	ASN	LEU	LEU	E	E	2 - 345	2 - 345
2	23	ASN	ASN	LEU	LEU	F	F	2 - 345	2 - 345
1	24	ASN	ASN	LEU	LEU	E	E	4 - 345	4 - 345
2	24	ASN	ASN	LEU	LEU	G	G	4 - 345	4 - 345
1	25	ASN	ASN	LEU	LEU	E	E	2 - 345	2 - 345
2	25	ASN	ASN	LEU	LEU	H	H	2 - 345	2 - 345
1	26	ASN	ASN	LEU	LEU	F	F	4 - 345	4 - 345
2	26	ASN	ASN	LEU	LEU	G	G	4 - 345	4 - 345
1	27	MET	MET	LEU	LEU	F	F	1 - 345	1 - 345
2	27	MET	MET	LEU	LEU	H	H	1 - 345	1 - 345
1	28	ASN	ASN	LEU	LEU	G	G	4 - 345	4 - 345
2	28	ASN	ASN	LEU	LEU	H	H	4 - 345	4 - 345

NCS ensembles :

#1: Protein

AlfC

Mass: 39326.727 Da / Num. of mol.: 8 / Mutation: N243A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Lactobacillus casei (bacteria) / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: K0NB39, UniProt: A0A422MHI3*PLUS,

alpha-L-fucosidase

#2: Sugar

ChemComp-FUL / beta-L-fucopyranose / beta-L-fucose / 6-deoxy-beta-L-galactopyranose / L-fucose / fucose / 6-DEOXY-BETA-L-GALACTOSE /

Fucose

Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₂O₅

#3: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 761 / 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: 2.34 Å³/Da / Density % sol: 47.33 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 250 nL 20 mg/mL AlfC + 250 nL mother liquor (18% w/v PEG3350, 0.1 M Bis-Tris propane, pH 7, 20 mM sodium/potassium phosphate, 1% v/v glycerol), crystals appeared after five days, harvested ...Details: 250 nL 20 mg/mL AlfC + 250 nL mother liquor (18% w/v PEG3350, 0.1 M Bis-Tris propane, pH 7, 20 mM sodium/potassium phosphate, 1% v/v glycerol), crystals appeared after five days, harvested in mother liquor + 20% v/v glycerol + 5 mM 4-NP-Fuc for ~1 minute, flash-cooled in liquid nitrogen

Crystal

Density Matthews: 2.34 Å³/Da / Density % sol: 47.33 %

Crystal grow

Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 250 nL 20 mg/mL AlfC + 250 nL mother liquor (18% w/v PEG3350, 0.1 M Bis-Tris propane, pH 7, 20 mM sodium/potassium phosphate, 1% v/v glycerol), crystals appeared after five days, harvested ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-B / Wavelength: 1.03321 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 5, 2018

Radiation

Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.03321 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.645
1	1	-L, -K, -H	2	0.355

Reflection

Resolution: 2→47.75 Å / Num. obs: 177005 / % possible obs: 91.5 % / Redundancy: 2.3 % / CC_1/2: 0.998 / R_merge(I) obs: 0.055 / R_pim(I) all: 0.042 / R_rim(I) all: 0.07 / Net I/σ(I): 8.5

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
2-2.03	1.8	0.827	9872	5559	0.462	0.675	1.074	0.7	58.4
10.95-47.75	2.5	0.016	2928	1173	0.999	0.012	0.021	26	96.4

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XDS		data reduction
Aimless	0.7.3	data scaling
MOLREP		phasing
REFMAC	5.8.0238	refinement
PDB_EXTRACT	3.24	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 6O18

6o18

Resolution: 2→47.75 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.957 / SU B: 7.235 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.039
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2426	9045	5.1 %	RANDOM
R_work	0.23	-	-	-
obs	0.2307	167908	91.28 %	-

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å

Displacement parameters

B_iso max: 122.2 Å² / B_iso mean: 48.55 Å² / B_iso min: 24.53 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.9 Å²	-0 Å²	19.73 Å²
2-	-	-9.95 Å²	0 Å²
3-	-	-	14.84 Å²

Refinement step

Cycle: final / Resolution: 2→47.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20791	0	88	761	21640
B_iso mean	-	-	55.73	48.19	-
Num. residues	-	-	-	-	2590

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	21454
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.017	18580
X-RAY DIFFRACTION	r_angle_refined_deg	1.46	1.644	29146
X-RAY DIFFRACTION	r_angle_other_deg	1.337	1.583	43274
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.942	5	2572
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.868	24.264	1175
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.405	15	3383
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	8.552	15	64
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	2679
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	24314
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	4595

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	11160	0.08
1	2	B	11160	0.08
2	1	A	11147	0.08
2	2	C	11147	0.08
3	1	A	11165	0.08
3	2	D	11165	0.08
4	1	A	11301	0.08
4	2	E	11301	0.08
5	1	A	11159	0.08
5	2	F	11159	0.08
6	1	A	10970	0.08
6	2	G	10970	0.08
7	1	A	11146	0.08
7	2	H	11146	0.08
8	1	B	11195	0.06
8	2	C	11195	0.06
9	1	B	11209	0.07
9	2	D	11209	0.07
10	1	B	11219	0.06
10	2	E	11219	0.06
11	1	B	11130	0.07
11	2	F	11130	0.07
12	1	B	10931	0.07
12	2	G	10931	0.07
13	1	B	11117	0.07
13	2	H	11117	0.07
14	1	C	11258	0.06
14	2	D	11258	0.06
15	1	C	11200	0.07
15	2	E	11200	0.07
16	1	C	11212	0.07
16	2	F	11212	0.07
17	1	C	11055	0.07
17	2	G	11055	0.07
18	1	C	11139	0.07
18	2	H	11139	0.07
19	1	D	11233	0.07
19	2	E	11233	0.07
20	1	D	11205	0.07
20	2	F	11205	0.07
21	1	D	10987	0.07
21	2	G	10987	0.07
22	1	D	11211	0.07
22	2	H	11211	0.07
23	1	E	11121	0.08
23	2	F	11121	0.08
24	1	E	11015	0.07
24	2	G	11015	0.07
25	1	E	11230	0.07
25	2	H	11230	0.07
26	1	F	11048	0.07
26	2	G	11048	0.07
27	1	F	11172	0.07
27	2	H	11172	0.07
28	1	G	10961	0.07
28	2	H	10961	0.07

LS refinement shell

Resolution: 1.999→2.051 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	1.381	389	-
R_work	1.187	7904	-
all	-	8293	-
obs	-	-	57.93 %

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	1.3621	0.4246	-0.1037	1.5111	0.3752	0.9061	0.0926	-0.0995	0.1764	0.2737	-0.126	0.2682	-0.0445	-0.1257	0.0335	0.0752	-0.0144	0.0179	0.2459	-0.0106	0.1743	-21.482	0.264	3.27
2	1.1833	0.0805	-0.1991	1.2945	-0.1429	0.6729	0.0111	-0.0915	0.0306	0.1533	-0.0246	-0.2106	0.0066	0.1359	0.0134	0.0299	0.0047	-0.0762	0.2663	-0.0029	0.2784	-4.536	40.619	17.819
3	0.9278	0.6383	-0.1094	1.9306	-0.2401	1.3307	-0.1582	0.262	-0.2686	-0.4324	0.1004	-0.1065	0.314	-0.0142	0.0578	0.1591	-0.04	-0.0051	0.3588	-0.0732	0.2576	-17.458	-29.404	-23.375
4	1.2391	-0.196	-0.354	1.2202	0.2829	0.8805	0.0359	0.3039	0.0077	-0.1794	-0.0273	0.2169	-0.0447	-0.1438	-0.0087	0.0369	-0.0023	-0.0841	0.3329	0.0147	0.3128	39.742	44.732	0.757
5	0.9148	0.2868	-0.1845	2.0952	-1.0965	1.8601	-0.1329	0.1344	-0.2252	-0.3963	-0.0978	-0.6822	0.3425	0.2117	0.2306	0.1026	0.0271	0.097	0.3157	0.0007	0.3901	18.806	-9.675	-23.243
6	1.0982	-0.2682	-0.1925	1.5	-0.1195	0.6529	0.0778	0.2857	0.0886	-0.2662	-0.0885	-0.0124	-0.0481	-0.0664	0.0108	0.0704	0.0044	-0.0435	0.3179	0.0349	0.2676	57.709	82.267	-1.674
7	1.2799	0.2851	0.1686	1.3881	-0.5615	1.3345	-0.0473	0.1531	0.3068	-0.0634	0.0883	0.1901	-0.2863	-0.188	-0.0409	0.1422	0.0354	-0.0385	0.3655	0.06	0.2536	-7.956	18.678	-30.809
8	1.1664	0.49	-0.1061	1.1882	-0.0114	0.8092	0.1289	-0.4004	-0.0275	0.4775	-0.1539	-0.0683	-0.0595	0.1069	0.0249	0.2376	-0.0691	-0.0491	0.3939	0.0117	0.3165	-21.663	72.557	37.103

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 345
2	X-RAY DIFFRACTION	2	B	1 - 345
3	X-RAY DIFFRACTION	3	C	2 - 345
4	X-RAY DIFFRACTION	4	D	1 - 345
5	X-RAY DIFFRACTION	5	E	2 - 345
6	X-RAY DIFFRACTION	6	F	1 - 345
7	X-RAY DIFFRACTION	7	G	1 - 345
8	X-RAY DIFFRACTION	8	H	1 - 345

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Yorodumi