PDB-7xsh: Crystal structure of ClAgl29B bound with L-glucose

ID or keywords:

Entry

Database: PDB / ID: 7xsh

Title

Crystal structure of ClAgl29B bound with L-glucose

Components

Alpha-L-fucosidase

Keywords

HYDROLASE / Glycoside hydrolase

Function / homology

Function and homology information

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

Biological species

Cecembia lonarensis LW9 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.708 Å

Authors

Shishiuchi, R. / Kang, H. / Tagami, T. / Okuyama, M.

Funding support

Japan, 1items

Citation

Journal: Acs Omega / Year: 2022
Title: Discovery of alpha-l-Glucosidase Raises the Possibility of alpha-l-Glucosides in Nature.
Authors: Shishiuchi, R. / Kang, H. / Tagami, T. / Ueda, Y. / Lang, W. / Kimura, A. / Okuyama, M.

History

Deposition	May 14, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 18, 2023	Provider: repository / Type: Initial release
Revision 1.1	Apr 3, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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	7xsh.cif.gz	258.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7xsh_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	7xsh_full_validation.pdf.gz	1 MB	Display
Data in XML	7xsh_validation.xml.gz	46.4 KB	Display
Data in CIF	7xsh_validation.cif.gz	68.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xs/7xsh ftp://data.pdbj.org/pub/pdb/validation_reports/xs/7xsh	HTTPS FTP

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Related structure data

Related structure data	7xsfC 7xsgC C: citing same article (ref.)
Similar structure data	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	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Alpha-L-fucosidase

B: Alpha-L-fucosidase

hetero molecules

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

1

A: Alpha-L-fucosidase

hetero molecules

B: Alpha-L-fucosidase

hetero molecules

defined by author&software
Evidence: gel filtration
136 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	72.393, 121.583, 166.372
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:

ID	Ens-ID	Details
1	1	A
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ASN / End label comp-ID: ASN / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 33 - 586 / Label seq-ID: 34 - 587

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein

Alpha-L-fucosidase / alpha-L-glucosidase

Mass: 67198.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Cecembia lonarensis LW9 (bacteria) / Gene: B879_03287 / Plasmid: pET28a / Production host:

Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: K1KV82

#2: Sugar

ChemComp-Z8T / beta-L-glucopyranose / beta-L-glucose / L-glucose / glucose

Type: L-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₂O₆ / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 5 types, 701 molecules

#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈O₇
#6: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 692 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Sequence details	GenBank EKB48090.1

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.72 Å³/Da / Density % sol: 54.85 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5 Details: 0.1 M sodium citrate (pH 3.5), 5% PEG 20,000, 5% 2-propanol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 5, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.708→98.164 Å / Num. obs: 159024 / % possible obs: 99.8 % / Redundancy: 6.7 % / B_iso Wilson estimate: 27.15 Å² / CC_1/2: 0.999 / R_rim(I) all: 0.101 / R_sym value: 0.093 / Net I/σ(I): 17.44
Reflection shell	Resolution: 1.71→1.81 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.37 / Num. unique obs: 25291 / CC_1/2: 0.81 / R_rim(I) all: 0.942 / R_sym value: 0.863 / % possible all: 99.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0349	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: Apo form

Resolution: 1.708→46.598 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.953 / SU B: 2.15 / SU ML: 0.067 / Cross valid method: FREE R-VALUE / ESU R: 0.091 / ESU R Free: 0.089
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2016	7948	4.998 %
R_work	0.1789	151073	-
all	0.18	-	-
obs	-	159021	99.827 %

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: 24.522 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.261 Å²	-0 Å²	0 Å²
2-	-	1.425 Å²	-0 Å²
3-	-	-	-1.686 Å²

Refinement step

Cycle: LAST / Resolution: 1.708→46.598 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8872	0	76	692	9640

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	9263
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	8232
X-RAY DIFFRACTION	r_angle_refined_deg	1.287	1.635	12551
X-RAY DIFFRACTION	r_angle_other_deg	0.453	1.561	19278
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.564	5	1108
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	13.178	10	36
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.408	10	1567
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.146	10	453
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	1301
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	10430
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1882
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	1808
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.188	0.2	7676
X-RAY DIFFRACTION	r_nbtor_refined	0.183	0.2	4429
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	4618
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.125	0.2	581
X-RAY DIFFRACTION	r_metal_ion_refined	0.119	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.276	0.2	42
X-RAY DIFFRACTION	r_nbd_other	0.219	0.2	74
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.172	0.2	27
X-RAY DIFFRACTION	r_mcbond_it	2.076	2.5	4420
X-RAY DIFFRACTION	r_mcbond_other	2.075	2.5	4420
X-RAY DIFFRACTION	r_mcangle_it	3.083	3.732	5532
X-RAY DIFFRACTION	r_mcangle_other	3.083	3.733	5533
X-RAY DIFFRACTION	r_scbond_it	2.655	2.731	4843
X-RAY DIFFRACTION	r_scbond_other	2.654	2.732	4844
X-RAY DIFFRACTION	r_scangle_it	4.086	3.978	7019
X-RAY DIFFRACTION	r_scangle_other	4.086	3.979	7020
X-RAY DIFFRACTION	r_lrange_it	5.579	36.066	10751
X-RAY DIFFRACTION	r_lrange_other	5.491	34.754	10602
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.09	0.05	18939

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	0.09	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.09	0.05009

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
1.708-1.753	0.308	569	0.297	10850	0.298	11648	0.939	0.94	98.034	0.263
1.753-1.801	0.282	567	0.264	10778	0.265	11349	0.942	0.952	99.9648	0.227
1.801-1.853	0.27	555	0.246	10547	0.247	11104	0.944	0.957	99.982	0.207
1.853-1.91	0.235	536	0.219	10195	0.219	10733	0.96	0.966	99.9814	0.178
1.91-1.972	0.225	518	0.207	9859	0.208	10377	0.966	0.97	100	0.167
1.972-2.041	0.215	506	0.198	9594	0.199	10101	0.968	0.973	99.9901	0.163
2.041-2.118	0.199	486	0.185	9258	0.185	9744	0.974	0.977	100	0.154
2.118-2.204	0.207	471	0.183	8921	0.184	9395	0.972	0.979	99.9681	0.155
2.204-2.302	0.196	450	0.175	8544	0.176	8994	0.976	0.981	100	0.151
2.302-2.414	0.208	432	0.17	8223	0.172	8656	0.971	0.982	99.9884	0.147
2.414-2.544	0.21	410	0.171	7780	0.173	8190	0.971	0.982	100	0.147
2.544-2.698	0.194	390	0.16	7415	0.162	7805	0.978	0.984	100	0.14
2.698-2.884	0.193	367	0.158	6972	0.16	7339	0.978	0.985	100	0.141
2.884-3.114	0.178	341	0.159	6493	0.16	6835	0.98	0.985	99.9854	0.146
3.114-3.41	0.185	316	0.165	6000	0.166	6317	0.981	0.984	99.9842	0.156
3.41-3.81	0.175	289	0.16	5478	0.161	5768	0.98	0.985	99.9827	0.156
3.81-4.394	0.153	253	0.144	4838	0.145	5093	0.985	0.987	99.9607	0.146
4.394-5.37	0.185	218	0.155	4130	0.157	4350	0.986	0.988	99.954	0.162
5.37-7.544	0.246	172	0.205	3269	0.207	3441	0.976	0.982	100	0.204
7.544-46.598	0.214	102	0.201	1929	0.202	2045	0.979	0.979	99.3154	0.208

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