PDB-6l6b: X-ray structure of human galectin-10 in complex with L-fucose

ID or keywords:

Entry

Database: PDB / ID: 6l6b

Title

X-ray structure of human galectin-10 in complex with L-fucose

Components

Galectin-10

Keywords

SUGAR BINDING PROTEIN / beta-sandwich structure / lectin

Function / homology

Function and homology information

regulation of activated T cell proliferation / regulation of T cell cytokine production / T cell apoptotic process / regulation of T cell anergy / : / carbohydrate binding / identical protein binding / cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.802 Å

Authors

Kamitori, S.

Citation

Journal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Structures of human galectin-10/monosaccharide complexes demonstrate potential of monosaccharides as effectors in forming Charcot-Leyden crystals.
Authors: Itoh, A. / Nonaka, Y. / Nakakita, S.I. / Yoshida, H. / Nishi, N. / Nakamura, T. / Kamitori, S.

History

Deposition	Oct 28, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 4, 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 Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2	Nov 22, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: atom_type / chem_comp ...atom_type / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6l6b.cif.gz	48.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6l6b.ent.gz	30.5 KB	Display	PDB format
PDBx/mmJSON format	6l6b.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6l6b_validation.pdf.gz	774.6 KB	Display	wwPDB validaton report
Full document	6l6b_full_validation.pdf.gz	774.6 KB	Display
Data in XML	6l6b_validation.xml.gz	8.1 KB	Display
Data in CIF	6l6b_validation.cif.gz	10.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l6/6l6b ftp://data.pdbj.org/pub/pdb/validation_reports/l6/6l6b	HTTPS FTP

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Related structure data

Related structure data	6l64C 6l67C 6l68C 6l6aC 6l6cC 6l6dC 1qkqS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6l6a-1 6l67-1 5xro-1 5xrg-1 6a1t-1 6hjm-10 4gc2-1 6a1v-1 6m2a-d 5xrh-1 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: Galectin-10

hetero molecules

16.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Galectin-10

hetero molecules

A: Galectin-10

hetero molecules

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

Unit cell

Length a, b, c (Å)	48.820, 48.820, 261.030
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	179
Space group name H-M	P6₅22

Components on special symmetry positions

ID	Model	Components
1	1	A-351- HOH
2	1	A-362- HOH

#1: Protein

Galectin-10 / Gal-10 / Charcot-Leyden crystal protein / CLC / Eosinophil lysophospholipase / Lysolecithin acylhydrolase

Mass: 16644.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: CLC, LGALS10, LGALS10A / Production host:

Escherichia coli (E. coli) / References: UniProt: Q05315

#2: Sugar

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

Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₂O₅ / Feature type: SUBJECT OF INVESTIGATION

#3: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H₂O

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: 2.7 Å³/Da / Density % sol: 54.4 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.6 M ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 10 % (v/v) 1,4-dioxane

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
Detector	Type: RIGAKU / Detector: IMAGE PLATE / Date: Oct 5, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.8→19.55 Å / Num. obs: 18129 / % possible obs: 99.5 % / Redundancy: 18.6 % / CC_1/2: 0.997 / Net I/σ(I): 15.1
Reflection shell	Resolution: 1.8→1.85 Å / Num. unique obs: 1223 / CC_1/2: 0.977

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0253	refinement
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1QKQ

1qkq

Resolution: 1.802→19.546 Å / Cor.coef. F_o:F_c: 0.931 / Cor.coef. F_o:F_c free: 0.908 / SU B: 2.71 / SU ML: 0.085 / Cross valid method: FREE R-VALUE / ESU R: 0.124 / ESU R Free: 0.126
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2553	926	5.108 %
R_work	0.2126	-	-
all	0.215	-	-
obs	-	18129	99.544 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 16.868 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.046 Å²	0.023 Å²	0 Å²
2-	-	0.046 Å²	0 Å²
3-	-	-	-0.148 Å²

Refinement step

Cycle: LAST / Resolution: 1.802→19.546 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1159	0	11	74	1244

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.013	1198
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	1096
X-RAY DIFFRACTION	r_angle_refined_deg	1.419	1.661	1621
X-RAY DIFFRACTION	r_angle_other_deg	1.21	1.584	2551
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	9.106	5	141
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.19	22.5	64
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.607	15	212
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.101	15	7
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	153
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1313
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	256
X-RAY DIFFRACTION	r_nbd_refined	0.171	0.15	175
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.162	0.15	986
X-RAY DIFFRACTION	r_nbtor_refined	0.16	0.15	549
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.074	0.15	578
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.128	0.15	57
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.098	0.15	11
X-RAY DIFFRACTION	r_nbd_other	0.157	0.15	32
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.151	0.15	18
X-RAY DIFFRACTION	r_mcbond_it	0.982	1.64	567
X-RAY DIFFRACTION	r_mcbond_other	0.982	1.637	566
X-RAY DIFFRACTION	r_mcangle_it	1.595	2.448	707
X-RAY DIFFRACTION	r_mcangle_other	1.594	2.451	708
X-RAY DIFFRACTION	r_scbond_it	1.484	1.848	631
X-RAY DIFFRACTION	r_scbond_other	1.483	1.848	631
X-RAY DIFFRACTION	r_scangle_it	2.396	2.687	914
X-RAY DIFFRACTION	r_scangle_other	2.394	2.688	915
X-RAY DIFFRACTION	r_lrange_it	3.625	18.592	1239
X-RAY DIFFRACTION	r_lrange_other	3.617	18.473	1231

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
1.802-1.848	0.365	58	0.312	1165	0.315	1277	0.807	0.854	95.7713	0.249
1.848-1.898	0.329	70	0.238	1190	0.243	1260	0.878	0.906	100	0.214
1.898-1.953	0.241	70	0.209	1173	0.211	1243	0.932	0.93	100	0.186
1.953-2.012	0.292	59	0.209	1110	0.213	1169	0.897	0.925	100	0.187
2.012-2.077	0.253	50	0.206	1110	0.208	1160	0.911	0.937	100	0.187
2.077-2.149	0.233	70	0.198	1064	0.2	1134	0.937	0.944	100	0.184
2.149-2.229	0.248	59	0.211	1058	0.213	1117	0.928	0.937	100	0.196
2.229-2.319	0.306	50	0.211	985	0.216	1035	0.885	0.92	100	0.198
2.319-2.421	0.299	49	0.219	968	0.222	1017	0.884	0.914	100	0.203
2.421-2.537	0.267	45	0.199	927	0.202	972	0.91	0.942	100	0.187
2.537-2.672	0.274	48	0.214	891	0.217	939	0.921	0.932	100	0.202
2.672-2.83	0.299	46	0.215	845	0.219	891	0.919	0.934	100	0.212
2.83-3.021	0.249	41	0.229	810	0.23	851	0.918	0.93	100	0.225
3.021-3.257	0.29	40	0.215	759	0.218	799	0.923	0.934	100	0.218
3.257-3.558	0.238	43	0.212	684	0.213	727	0.947	0.949	100	0.221
3.558-3.962	0.221	29	0.198	641	0.199	671	0.949	0.948	99.851	0.211
3.962-4.543	0.198	27	0.184	591	0.184	618	0.969	0.967	100	0.203
4.543-5.491	0.166	29	0.207	518	0.205	547	0.973	0.968	100	0.223
5.491-7.476	0.252	20	0.224	422	0.225	442	0.941	0.953	100	0.234
7.476-19.546	0.248	23	0.236	292	0.237	315	0.961	0.963	100	0.275

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