PDB-7rdo: Crystal structure of human galectin-3 CRD in complex with diselen...

ID or keywords:

Entry

Database: PDB / ID: 7rdo

Title

Crystal structure of human galectin-3 CRD in complex with diselenodigalactoside

Components

Galectin-3

Keywords

SUGAR BINDING PROTEIN / Galectin / carbohydrate-binding protein

Function / homology

Function and homology information

negative regulation of NK T cell activation / negative regulation of immunological synapse formation / disaccharide binding / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX2 regulates genes involved in differentiation of myeloid cells / regulation of T cell apoptotic process / mononuclear cell migration / receptor ligand inhibitor activity / positive regulation of mononuclear cell migration / negative regulation of endocytosis ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.99 Å

Authors

Kishor, C. / Go, R.M. / Blanchard, H.

Citation

Journal: Int J Mol Sci / Year: 2022
Title: Investigation of the Molecular Details of the Interactions of Selenoglycosides and Human Galectin-3.
Authors: Raics, M. / Balogh, A.K. / Kishor, C. / Timari, I. / Medrano, F.J. / Romero, A. / Go, R.M. / Blanchard, H. / Szilagyi, L. / E Kover, K. / Feher, K.

History

Deposition	Jul 10, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 13, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jul 20, 2022	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7rdo.cif.gz	48.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7rdo.ent.gz	30 KB	Display	PDB format
PDBx/mmJSON format	7rdo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7rdo_validation.pdf.gz	1010.4 KB	Display	wwPDB validaton report
Full document	7rdo_full_validation.pdf.gz	1010.5 KB	Display
Data in XML	7rdo_validation.xml.gz	8.2 KB	Display
Data in CIF	7rdo_validation.cif.gz	10.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rd/7rdo ftp://data.pdbj.org/pub/pdb/validation_reports/rd/7rdo	HTTPS FTP

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Related structure data

Related structure data	7rdpC 6b8kS S: Starting model for refinement 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	#79 - Jul 2006 Amyloid-beta Precursor Protein similarity (1) #189 - Sep 2015 Amyloids similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (1)

Deposited unit

A: Galectin-3

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	34.906, 58.366, 63.059
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Galectin-3 / Gal-3 / 35 kDa lectin / Carbohydrate-binding protein 35 / CBP 35 / Galactose-specific lectin 3 / ...Gal-3 / 35 kDa lectin / Carbohydrate-binding protein 35 / CBP 35 / Galactose-specific lectin 3 / Galactoside-binding protein / GALBP / IgE-binding protein / L-31 / Laminin-binding protein / Lectin L-29 / Mac-2 antigen Mass: 15758.100 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS3, MAC2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P17931
#2: Chemical	ChemComp-4IW / (2R,3R,4S,5R,6S)-2-(hydroxymethyl)-6-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]diselanyl}oxane-3,4,5-triol (non-preferred name) Mass: 484.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₂₂O₁₀Se₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.04 Å³/Da / Density % sol: 39.65 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 31% PEG6000, 100 mM magnesium chloride, 8 mM BME, 100 mM Tris-HCl, pH 7.0,

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 19, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.953 Å / Relative weight: 1
Reflection	Resolution: 1.99→31.55 Å / Num. obs: 9155 / % possible obs: 99.5 % / Redundancy: 6 % / CC_1/2: 0.984 / Net I/σ(I): 11
Reflection shell	Resolution: 2→2.07 Å / Mean I/σ(I) obs: 7.9 / Num. unique obs: 884 / CC_1/2: 0.969

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6B8K

6b8k

Resolution: 1.99→31.55 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.923 / SU B: 4.054 / SU ML: 0.116 / Cross valid method: FREE R-VALUE / ESU R: 0.21 / ESU R Free: 0.19
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2468	458	5.003 %
R_work	0.1791	8697	-
all	0.182	-	-
obs	-	9155	99.252 %

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: 18.626 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.015 Å²	-0 Å²	-0 Å²
2-	-	0.01 Å²	0 Å²
3-	-	-	-0.025 Å²

Refinement step

Cycle: LAST / Resolution: 1.99→31.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1112	0	26	50	1188

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	1221
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	1165
X-RAY DIFFRACTION	r_angle_refined_deg	1.729	1.709	1667
X-RAY DIFFRACTION	r_angle_other_deg	1.243	1.644	2689
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.336	5	146
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.306	21.884	69
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.325	15	201
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.558	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	169
X-RAY DIFFRACTION	r_chiral_restr_other	0.019	0.2	4
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1360
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	288
X-RAY DIFFRACTION	r_nbd_refined	0.191	0.2	145
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.175	0.2	954
X-RAY DIFFRACTION	r_nbtor_refined	0.157	0.2	540
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	606
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.121	0.2	44
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.2	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.17	0.2	46
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.096	0.2	7
X-RAY DIFFRACTION	r_mcbond_it	1.504	1.716	569
X-RAY DIFFRACTION	r_mcbond_other	1.5	1.713	568
X-RAY DIFFRACTION	r_mcangle_it	2.17	2.557	714
X-RAY DIFFRACTION	r_mcangle_other	2.172	2.56	715
X-RAY DIFFRACTION	r_scbond_it	2.292	2.104	652
X-RAY DIFFRACTION	r_scbond_other	2.29	2.106	653
X-RAY DIFFRACTION	r_scangle_it	3.639	3.065	951
X-RAY DIFFRACTION	r_scangle_other	3.638	3.068	952
X-RAY DIFFRACTION	r_lrange_it	4.629	20.118	1158
X-RAY DIFFRACTION	r_lrange_other	4.56	20.028	1152

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.996-2.048	0.193	26	0.15	622	X-RAY DIFFRACTION	95.0147
2.048-2.104	0.298	39	0.169	577	X-RAY DIFFRACTION	97.0079
2.104-2.164	0.252	34	0.186	589	X-RAY DIFFRACTION	98.265
2.164-2.231	0.289	34	0.192	556	X-RAY DIFFRACTION	99.8308
2.231-2.304	0.222	31	0.184	575	X-RAY DIFFRACTION	99.6711
2.304-2.385	0.254	32	0.189	544	X-RAY DIFFRACTION	100
2.385-2.474	0.28	22	0.183	539	X-RAY DIFFRACTION	99.8221
2.474-2.575	0.274	28	0.18	512	X-RAY DIFFRACTION	100
2.575-2.689	0.353	18	0.192	513	X-RAY DIFFRACTION	100
2.689-2.82	0.29	9	0.195	468	X-RAY DIFFRACTION	100
2.82-2.971	0.296	30	0.197	456	X-RAY DIFFRACTION	100
2.971-3.151	0.232	24	0.178	433	X-RAY DIFFRACTION	100
3.151-3.367	0.265	22	0.18	392	X-RAY DIFFRACTION	100
3.367-3.635	0.235	21	0.164	385	X-RAY DIFFRACTION	100
3.635-3.979	0.158	16	0.171	355	X-RAY DIFFRACTION	100
3.979-4.444	0.182	18	0.141	321	X-RAY DIFFRACTION	100
4.444-5.122	0.171	12	0.151	294	X-RAY DIFFRACTION	100
5.122-6.251	0.258	18	0.203	244	X-RAY DIFFRACTION	100
6.251-8.748	0.35	13	0.23	201	X-RAY DIFFRACTION	100

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