PDB-8p1s: Bifidobacterium asteroides alpha-L-fucosidase (TT1819) in complex...

ID or keywords:

Entry

Database: PDB / ID: 8p1s

Title

Bifidobacterium asteroides alpha-L-fucosidase (TT1819) in complex with fucose.

Components

Bifidobacterium asteroides alpha-L-fucosidase (TT1819)

Keywords

SUGAR BINDING PROTEIN / glycosidase hydrolase / fucosidase / GH29

Function / homology

alpha-L-fucopyranose /

IMIDAZOLE

Function and homology information

Biological species

Bifidobacterium asteroides (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Owen, C.D. / Penner, M. / Gascuena, A.N. / Wu, H. / Hernando, P.J. / Monaco, S. / Le Gall, G. / Gardner, R. / Ndeh, D. / Urbanowicz, P.A. ...

Funding support

United Kingdom,

Spain, European Union, 4items

Organization	Grant number	Country
Biotechnology and Biological Sciences Research Council (BBSRC)	BB/P010660/1	United Kingdom
Spanish Ministry of Science, Innovation, and Universities	PID2019-109395GB-I00	Spain
H2020 Marie Curie Actions of the European Commission	814102	European Union
UK Research and Innovation (UKRI)	BB/M029042/	United Kingdom

Citation

Journal: To Be Published
Title: Exploring sequence, structure and function of microbial fucosidases from glycoside hydrolase GH29 family
Authors: Owen, C.D. / Penner, M. / Gascuena, A.N. / Wu, H. / Hernando, P.J. / Monaco, S. / Le Gall, G. / Gardner, R. / Ndeh, D. / Urbanowicz, P.A. / Spencer, D.I.R. / Walsh, M.A. / Angulo, J. / Juge, N.

History

Deposition	May 12, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 22, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8p1s.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb8p1s.ent.gz	684.5 KB	Display	PDB format
PDBx/mmJSON format	8p1s.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/p1/8p1s ftp://data.pdbj.org/pub/pdb/validation_reports/p1/8p1s	HTTPS FTP

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Related structure data

Related structure data	8p1rC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#75 - Mar 2006 Tissue Factor similarity (1) #134 - Feb 2011 Integrin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

A: Bifidobacterium asteroides alpha-L-fucosidase (TT1819)

B: Bifidobacterium asteroides alpha-L-fucosidase (TT1819)

C: Bifidobacterium asteroides alpha-L-fucosidase (TT1819)

D: Bifidobacterium asteroides alpha-L-fucosidase (TT1819)

E: Bifidobacterium asteroides alpha-L-fucosidase (TT1819)

F: Bifidobacterium asteroides alpha-L-fucosidase (TT1819)

hetero molecules

235 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	89.058, 142.765, 167.202
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:

Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 22 - 362 / Label seq-ID: 2 - 342

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30

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Protein / Sugars , 2 types, 12 molecules ABCDEF

#1: Protein

Bifidobacterium asteroides alpha-L-fucosidase (TT1819)

Mass: 38867.016 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bifidobacterium asteroides (bacteria) / Production host:

Escherichia coli (E. coli)

#3: Sugar

ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose /

Fucose

Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₆H₁₂O₅ / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 5 types, 743 molecules

#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#5: Chemical	ChemComp-IMD / IMIDAZOLE / Imidazole Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₅N₂
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 733 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.32 Å³/Da / Density % sol: 46.97 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.12M Diethylene glycol; 0.12M Triethylene glycol; 0.12M Tetraethylene glycol; 0.12M Pentaethylene glycol, 0.1M Tris (base); BICINE pH 8.5, 10% v/v MPD; 10% PEG 1000; 10% w/v PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I24 / Wavelength: 0.97625 Å

Detector

Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 5, 2017

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97625 Å / Relative weight: 1

Reflection

Resolution: 1.9→108.56 Å / Num. obs: 167861 / % possible obs: 100 % / Redundancy: 17.5 % / CC_1/2: 0.998 / R_merge(I) obs: 0.246 / R_pim(I) all: 0.086 / R_rim(I) all: 0.262 / Net I/σ(I): 9.2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all
10.41-108.56	15.5	0.051	167861	0.999	0.018	0.054
1.9-1.93	14.9	9.946	8235	0.215	3.866	10.726

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0405	refinement
REFMAC	5.8.0405	refinement
xia2		data reduction
DIALS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→83.741 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.96 / SU B: 9.396 / SU ML: 0.123 / Cross valid method: FREE R-VALUE / ESU R: 0.142 / ESU R Free: 0.131
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2069	8366	4.988 %
R_work	0.1689	159354	-
all	0.171	-	-
obs	-	167720	99.95 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 38.507 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.975 Å²	-0 Å²	0 Å²
2-	-	1.839 Å²	-0 Å²
3-	-	-	0.136 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→83.741 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16170	0	118	733	17021

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.012	16838
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	15015
X-RAY DIFFRACTION	r_angle_refined_deg	1.924	1.648	22849
X-RAY DIFFRACTION	r_angle_other_deg	0.646	1.578	34629
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.668	5	2024
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	14.914	5	77
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.236	10	2703
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.697	10	872
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	2344
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	19883
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4061
X-RAY DIFFRACTION	r_nbd_refined	0.229	0.2	3177
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.194	0.2	14296
X-RAY DIFFRACTION	r_nbtor_refined	0.188	0.2	8427
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	8621
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.15	0.2	843
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.061	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.238	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.308	0.2	53
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.228	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	3.282	2.585	8095
X-RAY DIFFRACTION	r_mcbond_other	3.273	2.586	8095
X-RAY DIFFRACTION	r_mcangle_it	4.192	4.621	10118
X-RAY DIFFRACTION	r_mcangle_other	4.192	4.622	10119
X-RAY DIFFRACTION	r_scbond_it	4.595	2.902	8743
X-RAY DIFFRACTION	r_scbond_other	4.595	2.902	8744
X-RAY DIFFRACTION	r_scangle_it	6.302	5.175	12731
X-RAY DIFFRACTION	r_scangle_other	6.302	5.175	12732
X-RAY DIFFRACTION	r_lrange_it	7.313	25.577	19434
X-RAY DIFFRACTION	r_lrange_other	7.309	25.537	19338
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.066	0.05	11826
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.063	0.05	11854
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.067	0.05	11778
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.067	0.05	11801
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.074	0.05	11718
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.065	0.05	11787
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.066	0.05	11786
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.06	0.05	11855
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.07	0.05	11746
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.06	0.05	11830
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.053	0.05	11888
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.058	0.05	11818
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.055	0.05	12002
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.057	0.05	11981
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.058	0.05	11787

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.06616	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.06616	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.06284	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.06284	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.06652	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.06652	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.0672	0.05009
4	8	A	X-RAY DIFFRACTION	Local ncs	0.0672	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.07374	0.05009
5	10	A	X-RAY DIFFRACTION	Local ncs	0.07374	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.06508	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.06508	0.0501
7	13	A	X-RAY DIFFRACTION	Local ncs	0.06577	0.0501
7	14	A	X-RAY DIFFRACTION	Local ncs	0.06577	0.0501
8	15	A	X-RAY DIFFRACTION	Local ncs	0.0599	0.0501
8	16	A	X-RAY DIFFRACTION	Local ncs	0.0599	0.0501
9	17	A	X-RAY DIFFRACTION	Local ncs	0.06958	0.0501
9	18	A	X-RAY DIFFRACTION	Local ncs	0.06958	0.0501
10	19	A	X-RAY DIFFRACTION	Local ncs	0.06027	0.0501
10	20	A	X-RAY DIFFRACTION	Local ncs	0.06027	0.0501
11	21	A	X-RAY DIFFRACTION	Local ncs	0.05257	0.0501
11	22	A	X-RAY DIFFRACTION	Local ncs	0.05257	0.0501
12	23	A	X-RAY DIFFRACTION	Local ncs	0.0579	0.0501
12	24	A	X-RAY DIFFRACTION	Local ncs	0.0579	0.0501
13	25	A	X-RAY DIFFRACTION	Local ncs	0.05467	0.0501
13	26	A	X-RAY DIFFRACTION	Local ncs	0.05467	0.0501
14	27	A	X-RAY DIFFRACTION	Local ncs	0.05689	0.0501
14	28	A	X-RAY DIFFRACTION	Local ncs	0.05689	0.0501
15	29	A	X-RAY DIFFRACTION	Local ncs	0.05826	0.0501
15	30	A	X-RAY DIFFRACTION	Local ncs	0.05826	0.0501

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.9-1.949	0.356	636	0.349	11564	0.349	12233	0.883	0.893	99.7302	0.35
1.949-2.003	0.332	588	0.32	11399	0.321	11995	0.901	0.907	99.9333	0.318
2.003-2.061	0.325	632	0.289	11036	0.291	11676	0.917	0.929	99.9315	0.289
2.061-2.124	0.273	569	0.258	10759	0.259	11333	0.944	0.947	99.9559	0.253
2.124-2.194	0.271	572	0.223	10395	0.226	10967	0.943	0.962	100	0.213
2.194-2.271	0.224	466	0.2	10160	0.201	10630	0.963	0.971	99.9624	0.185
2.271-2.356	0.235	515	0.186	9758	0.189	10281	0.962	0.976	99.9222	0.168
2.356-2.452	0.232	471	0.164	9407	0.167	9882	0.965	0.983	99.9595	0.144
2.452-2.561	0.218	467	0.155	9059	0.158	9528	0.972	0.986	99.979	0.136
2.561-2.686	0.203	457	0.152	8642	0.155	9099	0.975	0.987	100	0.132
2.686-2.831	0.205	413	0.152	8240	0.155	8654	0.974	0.986	99.9884	0.132
2.831-3.003	0.201	408	0.156	7805	0.159	8215	0.975	0.985	99.9757	0.138
3.003-3.21	0.195	397	0.16	7319	0.162	7717	0.975	0.985	99.987	0.146
3.21-3.467	0.203	349	0.163	6857	0.165	7207	0.976	0.985	99.9861	0.154
3.467-3.797	0.199	334	0.155	6343	0.157	6677	0.979	0.988	100	0.149
3.797-4.244	0.148	314	0.12	5743	0.121	6057	0.987	0.992	100	0.119
4.244-4.899	0.138	256	0.112	5103	0.114	5359	0.989	0.993	100	0.116
4.899-5.994	0.197	227	0.144	4354	0.147	4582	0.98	0.99	99.9782	0.146
5.994-8.456	0.185	192	0.147	3403	0.149	3599	0.984	0.989	99.8889	0.152
8.456-83.741	0.171	103	0.175	2008	0.175	2112	0.984	0.976	99.9527	0.187

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	1.5948	-0.0956	0.2545	0.8867	0.2081	1.3436	0.0252	-0.1776	-0.0357	0.1075	-0.0136	-0.0494	0.009	0.1456	-0.0116	0.0143	-0.0093	-0.0074	0.049	0.011	0.0121	31.995	5.4698	-25.3981
2	1.4879	-0.0349	0.1602	1.3021	0.1146	1.1429	-0.0093	0.0999	0.2436	-0.0988	-0.0334	0.1461	-0.1963	-0.1521	0.0427	0.041	0.0293	-0.0241	0.0307	0.0083	0.1073	-12.4247	27.3068	-57.1476
3	1.8257	-0.0302	-0.0471	1.1643	-0.0367	1.1075	-0.015	-0.3342	-0.1043	0.1875	-0.0181	0.1213	0.0709	-0.1831	0.0331	0.04	-0.0173	0.0314	0.0971	0.0048	0.0375	-9.1936	1.0062	-22.8086
4	1.3684	0.1416	-0.1021	1.0192	-0.0107	1.5593	0.0328	0.1398	-0.2674	-0.1012	-0.0187	0.1445	0.2657	-0.2427	-0.0141	0.0951	-0.0496	-0.0148	0.0589	-0.0395	0.1035	-11.2671	-15.865	-62.5679
5	1.4762	0.1456	0.1338	1.0476	0.1047	1.2131	0.0025	0.2335	0.2886	-0.1664	-0.002	-0.1334	-0.1896	0.1908	-0.0005	0.0577	-0.0281	0.0267	0.0789	0.0656	0.1221	28.7232	27.8399	-62.325
6	1.3266	0.1227	0.0075	1.1346	-0.2613	1.2732	0.0436	0.2234	-0.336	-0.1496	-0.0298	-0.2206	0.3037	0.2735	-0.0139	0.1189	0.0653	0.0303	0.0988	-0.0695	0.1515	30.2504	-15.5723	-63.5525

Refinement TLS group

Selection: ALL

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Protein / Sugars , 2 types, 12 molecules ABCDEF

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Non-polymers , 5 types, 743 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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