PDB-6o1c: Alpha-L-fucosidase AlfC D200A mutant in complex with 4-nitropheny...

ID or keywords:

Entry

Database: PDB / ID: 6o1c

Title

Alpha-L-fucosidase AlfC D200A mutant in complex with 4-nitrophenyl-a-L-fucopyranoside substrate

Components

AlfC

Keywords

HYDROLASE / Fucosidase / substrate / 4NP-Fuc / 4-nitrophenyl-a-L-fucopyranoside

Function / homology

Function and homology information

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

Biological species

Lactobacillus casei (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.6 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 19, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 19, 2020	Provider: repository / Type: Initial release
Revision 2.0	Jul 29, 2020	Group: Atomic model / Derived calculations / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	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 2.2	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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PDBx/mmCIF format	6o1c.cif.gz	1023.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6o1c.ent.gz	869.8 KB	Display	PDB format
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Validation report

Summary document	6o1c_validation.pdf.gz	2.4 MB	Display	wwPDB validaton report
Full document	6o1c_full_validation.pdf.gz	2.4 MB	Display
Data in XML	6o1c_validation.xml.gz	94.3 KB	Display
Data in CIF	6o1c_validation.cif.gz	123.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o1/6o1c ftp://data.pdbj.org/pub/pdb/validation_reports/o1/6o1c	HTTPS FTP

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Related structure data

Related structure data	6o18SC 6o1aC 6o1iC 6o1jC 6oheC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6o1j-2 6o1i-1 6o1j-3 6o1i-2 6o1a-1 6o1a-2 6o18-2 6o1j-1 6o18-1 6ohe-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) 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

Deposited unit

A: AlfC

B: AlfC

C: AlfC

D: AlfC

E: AlfC

F: AlfC

G: AlfC

H: AlfC

hetero molecules

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

1

A: AlfC

D: AlfC

E: AlfC

G: AlfC

hetero molecules

defined by author
Evidence: equilibrium centrifugation, Gel filtration, native mass spectrometry, and analytical ultracentrifugation support the existence of tetramers in solution.
158 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: AlfC

C: AlfC

F: 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)	89.734, 139.079, 263.373
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

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	ASN	ASN	ARG	ARG	A	A	2 - 344	2 - 344
2	1	ASN	ASN	ARG	ARG	B	B	2 - 344	2 - 344
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	ASN	ASN	LEU	LEU	A	A	2 - 345	2 - 345
2	3	ASN	ASN	LEU	LEU	D	D	2 - 345	2 - 345
1	4	ASP	ASP	LEU	LEU	A	A	3 - 345	3 - 345
2	4	ASP	ASP	LEU	LEU	E	E	3 - 345	3 - 345
1	5	ASP	ASP	ARG	ARG	A	A	3 - 344	3 - 344
2	5	ASP	ASP	ARG	ARG	F	F	3 - 344	3 - 344
1	6	ASP	ASP	LEU	LEU	A	A	3 - 345	3 - 345
2	6	ASP	ASP	LEU	LEU	G	G	3 - 345	3 - 345
1	7	VAL	VAL	LEU	LEU	A	A	5 - 345	5 - 345
2	7	VAL	VAL	LEU	LEU	H	H	5 - 345	5 - 345
1	8	ASN	ASN	ASN	ASN	B	B	2 - 343	2 - 343
2	8	ASN	ASN	ASN	ASN	C	C	2 - 343	2 - 343
1	9	ASN	ASN	ARG	ARG	B	B	2 - 344	2 - 344
2	9	ASN	ASN	ARG	ARG	D	D	2 - 344	2 - 344
1	10	ASP	ASP	ASN	ASN	B	B	3 - 343	3 - 343
2	10	ASP	ASP	ASN	ASN	E	E	3 - 343	3 - 343
1	11	ASP	ASP	ARG	ARG	B	B	3 - 344	3 - 344
2	11	ASP	ASP	ARG	ARG	F	F	3 - 344	3 - 344
1	12	ASP	ASP	ASN	ASN	B	B	3 - 343	3 - 343
2	12	ASP	ASP	ASN	ASN	G	G	3 - 343	3 - 343
1	13	VAL	VAL	ARG	ARG	B	B	5 - 344	5 - 344
2	13	VAL	VAL	ARG	ARG	H	H	5 - 344	5 - 344
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	ASP	ASP	LEU	LEU	C	C	3 - 345	3 - 345
2	15	ASP	ASP	LEU	LEU	E	E	3 - 345	3 - 345
1	16	ASP	ASP	ASN	ASN	C	C	3 - 343	3 - 343
2	16	ASP	ASP	ASN	ASN	F	F	3 - 343	3 - 343
1	17	ASP	ASP	LEU	LEU	C	C	3 - 345	3 - 345
2	17	ASP	ASP	LEU	LEU	G	G	3 - 345	3 - 345
1	18	VAL	VAL	LEU	LEU	C	C	5 - 345	5 - 345
2	18	VAL	VAL	LEU	LEU	H	H	5 - 345	5 - 345
1	19	ASP	ASP	LEU	LEU	D	D	3 - 345	3 - 345
2	19	ASP	ASP	LEU	LEU	E	E	3 - 345	3 - 345
1	20	ASP	ASP	ARG	ARG	D	D	3 - 344	3 - 344
2	20	ASP	ASP	ARG	ARG	F	F	3 - 344	3 - 344
1	21	ASP	ASP	LEU	LEU	D	D	3 - 345	3 - 345
2	21	ASP	ASP	LEU	LEU	G	G	3 - 345	3 - 345
1	22	VAL	VAL	LEU	LEU	D	D	5 - 345	5 - 345
2	22	VAL	VAL	LEU	LEU	H	H	5 - 345	5 - 345
1	23	ASP	ASP	ASN	ASN	E	E	3 - 343	3 - 343
2	23	ASP	ASP	ASN	ASN	F	F	3 - 343	3 - 343
1	24	ASP	ASP	LEU	LEU	E	E	3 - 345	3 - 345
2	24	ASP	ASP	LEU	LEU	G	G	3 - 345	3 - 345
1	25	VAL	VAL	LEU	LEU	E	E	5 - 345	5 - 345
2	25	VAL	VAL	LEU	LEU	H	H	5 - 345	5 - 345
1	26	ASP	ASP	ARG	ARG	F	F	3 - 344	3 - 344
2	26	ASP	ASP	ARG	ARG	G	G	3 - 344	3 - 344
1	27	VAL	VAL	ARG	ARG	F	F	5 - 344	5 - 344
2	27	VAL	VAL	ARG	ARG	H	H	5 - 344	5 - 344
1	28	VAL	VAL	LEU	LEU	G	G	5 - 345	5 - 345
2	28	VAL	VAL	LEU	LEU	H	H	5 - 345	5 - 345

NCS ensembles :

#1: Protein	AlfC Mass: 39325.742 Da / Num. of mol.: 8 / Mutation: D200A 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-JFZ / 4-nitrophenyl 6-deoxy-alpha-L-galactopyranoside / 4-nitrophenyl-alpha-L-fucose / 4-nitrophenyl 6-deoxy-alpha-L-galactoside / 4-nitrophenyl 6-deoxy-L-galactoside / 4-nitrophenyl 6-deoxy-galactoside Type: L-saccharide / Mass: 285.250 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₂H₁₅NO₇ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.61 Å³/Da / Density % sol: 52.91 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 250 nL 20 mg/mL AlfC D200Aof + 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, ...Details: 250 nL 20 mg/mL AlfC D200Aof + 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, were harvested in mother liquor + 20% v/v glycerol + 5 mM 4NP-Fuc for ~1 minute, flash-cooled in liquid nitrogen

Crystal

Density Matthews: 2.61 Å³/Da / Density % sol: 52.91 %

Crystal grow

Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 250 nL 20 mg/mL AlfC D200Aof + 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, ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL12-2 / Wavelength: 1.03317 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 14, 2019

Radiation

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

Radiation wavelength

Wavelength: 1.03317 Å / Relative weight: 1

Reflection

Resolution: 2.6→39.43 Å / Num. obs: 97990 / % possible obs: 96.7 % / Redundancy: 3.4 % / CC_1/2: 0.994 / R_merge(I) obs: 0.109 / R_pim(I) all: 0.068 / R_rim(I) all: 0.129 / Net I/σ(I): 6.3 / Num. measured all: 330144 / Scaling rejects: 6

Reflection shell

Diffraction-ID: 1 / Redundancy: 3.3 %

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	% possible all
2.6-2.64	1.367	4933	0.582	0.855	1.621	98.5
14.24-39.43	0.054	615	0.997	0.035	0.065	86.6

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XDS		data reduction
Aimless	0.7.1	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: 2.6→39.43 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.934 / SU B: 36.953 / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.954 / ESU R Free: 0.333
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2607	4998	5.1 %	RANDOM
R_work	0.2315	-	-	-
obs	0.233	92904	95.82 %	-

Solvent computation

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

Displacement parameters

B_iso max: 146.92 Å² / B_iso mean: 70.728 Å² / B_iso min: 38.54 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.38 Å²	-0 Å²	0 Å²
2-	-	3.03 Å²	-0 Å²
3-	-	-	-0.65 Å²

Refinement step

Cycle: final / Resolution: 2.6→39.43 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20562	0	160	232	20954
B_iso mean	-	-	77.81	62.29	-
Num. residues	-	-	-	-	2584

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	21363
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.017	18283
X-RAY DIFFRACTION	r_angle_refined_deg	1.385	1.646	29072
X-RAY DIFFRACTION	r_angle_other_deg	1.311	1.581	42535
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.613	5	2574
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.254	24.168	1154
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.609	15	3244
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	7.828	15	63
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	2674
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	24312
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4630

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	10947	0.07
1	2	B	10947	0.07
2	1	A	10890	0.08
2	2	C	10890	0.08
3	1	A	11179	0.05
3	2	D	11179	0.05
4	1	A	10854	0.07
4	2	E	10854	0.07
5	1	A	10710	0.08
5	2	F	10710	0.08
6	1	A	10705	0.07
6	2	G	10705	0.07
7	1	A	10458	0.09
7	2	H	10458	0.09
8	1	B	10898	0.06
8	2	C	10898	0.06
9	1	B	10842	0.07
9	2	D	10842	0.07
10	1	B	10679	0.07
10	2	E	10679	0.07
11	1	B	10795	0.06
11	2	F	10795	0.06
12	1	B	10589	0.06
12	2	G	10589	0.06
13	1	B	10496	0.08
13	2	H	10496	0.08
14	1	C	10901	0.06
14	2	D	10901	0.06
15	1	C	10714	0.08
15	2	E	10714	0.08
16	1	C	10750	0.07
16	2	F	10750	0.07
17	1	C	10598	0.07
17	2	G	10598	0.07
18	1	C	10613	0.07
18	2	H	10613	0.07
19	1	D	10811	0.06
19	2	E	10811	0.06
20	1	D	10700	0.08
20	2	F	10700	0.08
21	1	D	10642	0.07
21	2	G	10642	0.07
22	1	D	10499	0.08
22	2	H	10499	0.08
23	1	E	10712	0.08
23	2	F	10712	0.08
24	1	E	10627	0.07
24	2	G	10627	0.07
25	1	E	10498	0.09
25	2	H	10498	0.09
26	1	F	10498	0.07
26	2	G	10498	0.07
27	1	F	10535	0.08
27	2	H	10535	0.08
28	1	G	10346	0.08
28	2	H	10346	0.08

LS refinement shell

Resolution: 2.6→2.667 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.42	368	-
R_work	0.393	6954	-
all	-	7322	-
obs	-	-	97.85 %

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	2.1945	-0.2286	-0.4342	1.5164	-0.2168	1.41	-0.0357	0.2265	0.2947	-0.0946	0.1268	0.1155	-0.1349	0.0397	-0.0911	0.8572	-0.0274	0.0085	0.0481	0.0445	0.0545	6.249	-44.659	-5.887
2	1.2756	-0.336	0.2195	1.6448	-0.0135	2.4446	0.0942	-0.1889	-0.0651	0.1615	-0.0445	-0.2097	0.2068	0.4647	-0.0498	0.8462	-0.0435	-0.0264	0.1416	0.0162	0.0369	32.514	-52.781	-43.392
3	1.2439	0.4608	0.327	1.671	-0.4702	2.168	0.1106	0.1261	-0.0635	-0.2932	0.0185	0.1966	0.4284	-0.3201	-0.129	1.0061	-0.02	-0.0522	0.0854	-0.0054	0.0359	11.98	-55.324	-89.106
4	2.3057	0.6164	0.6352	1.6362	0.0548	1.6827	0.1519	-0.1353	-0.3855	0.2719	0.0684	-0.0599	0.4308	0.0489	-0.2203	0.9953	0.085	-0.0629	0.0249	0.0164	0.0789	8.357	-93.656	4.345
5	1.5889	0.0346	0.372	1.3776	0.2873	1.7362	-0.0677	0.3758	0.2039	-0.2306	0.0753	0.4556	-0.1309	-0.0615	-0.0077	0.9419	-0.0696	-0.1155	0.1116	0.0868	0.2002	-12.55	-76.223	-25.675
6	1.336	0.1256	-0.0391	1.4807	0.1824	2.0848	0.0401	0.1147	0.1496	0.0503	-0.054	-0.4634	-0.1623	0.8314	0.014	0.9359	-0.0768	0.0342	0.3577	0.0656	0.1778	43.538	-32.634	-78.407
7	2.108	0.1025	-0.1412	1.3262	0.2119	1.1095	-0.1697	-0.5372	-0.3208	0.4328	0.1135	0.439	0.304	-0.0696	0.0562	1.0946	0.1425	0.2522	0.1802	0.1273	0.254	-13.942	-64.289	23.161
8	1.3276	-0.2238	0.2724	1.6907	-0.5505	2.1515	0.07	-0.092	0.0378	-0.0578	0.2295	0.5833	-0.1943	-0.9893	-0.2994	0.9552	0.0705	0.0352	0.4851	0.1254	0.2227	-1.542	-34.617	-55.789

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 345
2	X-RAY DIFFRACTION	2	B	2 - 345
3	X-RAY DIFFRACTION	3	C	2 - 345
4	X-RAY DIFFRACTION	4	D	2 - 345
5	X-RAY DIFFRACTION	5	E	3 - 345
6	X-RAY DIFFRACTION	6	F	3 - 344
7	X-RAY DIFFRACTION	7	G	3 - 345
8	X-RAY DIFFRACTION	8	H	3 - 345

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Yorodumi