PDB-7n8g: Crystal structure of R20A-R22A human Galectin-7 mutant

ID or keywords:

Entry

Database: PDB / ID: 7n8g

Title

Crystal structure of R20A-R22A human Galectin-7 mutant

Components

Galectin-7

Keywords

SUGAR BINDING PROTEIN / human galectin-7 / dimer interface mutant

Function / homology

Function and homology information

Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / carbohydrate binding / apoptotic process / extracellular space / extracellular exosome / nucleus / cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.95 Å

Authors

Pham, N.T.H. / Calmettes, C. / Doucet, N.

Funding support

Canada,

United States, 6items

Organization	Grant number	Country
Natural Sciences and Engineering Research Council (NSERC, Canada)	RGPIN 2016-05557	Canada
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R01GM105978	United States
Other government	FRQ-S Research Scholar Senior Career Award (281993)	Canada
Other government	FRQ-S Junior 1 (251848)	Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)	RGPIN-2017-06091	Canada
Other government	FRQ-S Doctoral Training scholarship (287239)	Canada

Citation

Journal: To Be Published
Title: Crystal structure of R20A human Galectin-7 mutant
Authors: Pham, N.T.H. / Calmettes, C. / Doucet, N.

History

Deposition	Jun 14, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 25, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 25, 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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PDBx/mmCIF format	7n8g.cif.gz	175.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7n8g.ent.gz	140.6 KB	Display	PDB format
PDBx/mmJSON format	7n8g.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7n8g_validation.pdf.gz	462.1 KB	Display	wwPDB validaton report
Full document	7n8g_full_validation.pdf.gz	463.2 KB	Display
Data in XML	7n8g_validation.xml.gz	16 KB	Display
Data in CIF	7n8g_validation.cif.gz	22.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n8/7n8g ftp://data.pdbj.org/pub/pdb/validation_reports/n8/7n8g	HTTPS FTP

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Related structure data

Related structure data	7n4oC 7n57C 7n6cC 1bkzS 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

Deposited unit

A: Galectin-7

B: Galectin-7

hetero molecules

30.4 kDa, 2 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)	53.240, 64.960, 72.160
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Galectin-7 / Gal-7 / HKL-14 / PI7 / p53-induced gene 1 protein Mass: 14793.617 Da / Num. of mol.: 2 / Mutation: R20A, R22A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS7, PIG1, LGALS7B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P47929
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.13 Å³/Da / Density % sol: 42.32 %
Crystal grow	Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M NaCl, 0.1 M Tris pH 8, 20 % PEG 6000 ,17.5% Glycerol Temp details: Room temperature

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

CLSI

/ Beamline: 08B1-1 / Wavelength: 1.0332 Å

Detector

Type: RAYONIX MX300HE / Detector: CCD / Date: Feb 19, 2019 / Details: 16 tiled fiber-optic tapers

Radiation

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

Radiation wavelength

Wavelength: 1.0332 Å / Relative weight: 1

Reflection

Resolution: 1.95→48.29 Å / Num. obs: 18712 / % possible obs: 99.5 % / Redundancy: 9.7 % / CC_1/2: 0.998 / R_merge(I) obs: 0.07 / R_pim(I) all: 0.024 / R_rim(I) all: 0.074 / Net I/σ(I): 22.6

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	% possible all
1.95-2.02	9.9	0.229	10	1791	0.986	0.076	0.242	98.8
2.02-2.1	9.9	0.174	12.7	1843	0.991	0.057	0.183	98.9
2.1-2.2	9.9	0.137	15.7	1829	0.994	0.045	0.145	99.2
2.2-2.31	9.8	0.112	18.1	1857	0.995	0.037	0.118	99.1
2.31-2.46	9.9	0.097	20.6	1835	0.996	0.032	0.103	99.5
2.46-2.65	9.8	0.084	22.8	1883	0.997	0.028	0.089	99.8
2.65-2.91	9.8	0.074	25.6	1866	0.997	0.024	0.078	99.6
2.91-3.33	9.7	0.062	29.9	1891	0.998	0.021	0.066	99.8
3.33-4.2	9.6	0.057	33.9	1909	0.997	0.019	0.061	100
4.2-48.29	9.1	0.057	34.2	2018	0.998	0.02	0.06	99.9

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	5.89 Å	48.28 Å
Translation	5.89 Å	48.28 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2-4158	refinement
XDS		data reduction
XSCALE		data scaling
PHASER	2.7.12	phasing
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1bkz

1bkz

Resolution: 1.95→48.28 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.47 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2043	1257	6.72 %
R_work	0.1665	17448	-
obs	0.169	18705	99.43 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 135.37 Å² / B_iso mean: 30.3257 Å² / B_iso min: 8.65 Å²

Refinement step

Cycle: final / Resolution: 1.95→48.28 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2086	0	120	255	2461
B_iso mean	-	-	53.22	36.94	-
Num. residues	-	-	-	-	269

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	2254
X-RAY DIFFRACTION	f_angle_d	1.039	3055
X-RAY DIFFRACTION	f_dihedral_angle_d	14.468	844
X-RAY DIFFRACTION	f_chiral_restr	0.067	320
X-RAY DIFFRACTION	f_plane_restr	0.005	416

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 9

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.95-2.03	0.2303	135	0.201	1868	2003	99
2.03-2.12	0.2538	136	0.1775	1900	2036	99
2.12-2.23	0.233	137	0.1773	1893	2030	99
2.23-2.37	0.1919	137	0.1697	1902	2039	100
2.37-2.56	0.1843	140	0.1682	1945	2085	99
2.56-2.81	0.2153	139	0.1844	1938	2077	100
2.81-3.22	0.2293	141	0.1665	1944	2085	100
3.22-4.06	0.2104	143	0.1416	1986	2129	100
4.06-48.28	0.1706	149	0.1675	2072	2221	100

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	0.0276	0.0108	0.0611	0.1347	-0.0844	0.1799	-0.3845	0.2883	0.4427	0.1685	-0.1291	0.5799	-0.1131	-0.1512	-0.0108	0.2472	-0.0388	-0.0013	0.1357	0.0098	0.2815	-0.03	-29.419	-1.503
2	0.2167	-0.0536	0.0439	0.0483	0.0141	0.1238	0.1212	-0.1556	-0.3804	-0.4313	0.1498	0.1725	0.7545	-0.4101	0.0435	0.257	-0.0404	-0.0144	0.1995	0.035	0.1494	2.092	-31.698	-18.265
3	1.0574	0.0834	-0.1113	0.4156	0.1321	-0.0481	-0.1014	-0.023	0.0594	0.033	0.0994	-0.0206	0.031	-0.0306	-0.0605	0.0999	-0.0049	-0.0183	0.1311	0.0297	0.1271	3.971	-18.899	-2.022
4	0.0435	0.0738	0.0241	0.068	-0.0062	0.0126	0.0318	-0.0239	-0.2318	-0.0041	0.3941	0.0157	0.2145	0.601	-0	0.1828	-0.0246	0.023	0.2156	-0.025	0.1875	11.13	-35.456	-2.369
5	0.1952	-0.1193	-0.2019	0.0289	0.354	0.0763	0.003	-0.022	0.083	0.0113	0.0662	-0.0725	-0.0076	-0.0407	0.0175	0.0899	-0.0043	-0.0072	0.0938	0.0142	0.1422	12.954	-19.082	-4.642
6	0.6908	0.1788	-0.2673	-0.1117	-0.2514	0.1861	0.0553	0.1083	-0.1037	-0.0822	-0.0051	0.0412	-0.0787	-0.0564	0.0389	0.1007	-0.0083	-0.0112	0.1289	0.0214	0.1612	10.508	-15.07	-5.324
7	0.0578	0.0248	0.1543	0.3703	-0.0587	0.2324	0.0563	0.2121	0.1048	-0.1145	0.0135	-0.0314	-0.0491	0.0305	0.001	0.1414	-0.0155	0.0044	0.1958	0.0418	0.1684	6.389	-17.487	-16.294
8	0.5461	0.2278	-0.2111	0.2225	0.0514	0.0358	-0.0816	0.0779	-0.0474	0.0681	0.0283	0.041	0.1505	-0.1717	0.0103	0.1297	-0.0132	0.0026	0.1364	0.0322	0.1317	3.859	-26.559	-8.092
9	-0.0181	0.0845	-0.0842	0.255	0.1558	0.3979	0.1164	0.1539	0.3574	-0.0615	-0.0672	-0.1974	0.1687	-0.1617	-0.0008	0.2084	0.0058	-0.0098	0.1981	-0.0022	0.2286	-7.187	-11.075	-32.331
10	0.2359	0.031	-0.2517	0.2698	-0.056	0.017	0.1098	-0.1361	0.2061	-0.0895	0.0372	0.0037	0.1944	0.0194	0.0018	0.1919	0.0059	0.0135	0.2069	-0.0045	0.1414	-3.033	-18.619	-23.997
11	0.9583	-0.669	0.6333	0.4291	-0.2197	0.8444	0.0299	0.1058	-0.0848	-0.1661	0.064	0.1732	0.3308	-0.2631	0.0718	0.1848	-0.0318	-0.0254	0.1599	0.0063	0.1584	-18.387	-19.167	-30.728
12	0.5241	-0.1156	0.111	0.5348	-0.3067	0.2871	0.0257	0.6723	-0.4689	-0.0716	0.0844	0.2624	0.6296	-0.2729	0.0757	0.4705	-0.0315	-0.0883	0.2488	-0.0693	0.2668	-14.857	-27.008	-41.085
13	0.9615	-0.1856	0.6931	0.2549	-0.0523	0.6662	-0.0832	-0.2792	-0.2882	0.0882	0.0617	0.5257	0.3084	-0.3362	0.1362	0.2468	-0.0915	0.0285	0.2657	0.0537	0.2491	-21.982	-22.234	-21.252
14	0.204	0.3114	-0.008	0.2994	-0.0785	0.3953	-0.1616	-0.1107	-0.1053	0.0067	0.0581	0.1081	0.3253	-0.0596	-0.0123	0.2146	-0.0037	-0.0124	0.144	0.0196	0.131	-8.985	-25.248	-21.455
15	0.8673	-0.0665	0.27	-0.0243	-0.0463	0.6531	0.0036	0.2266	-0.0089	-0.1489	-0.0353	-0.0233	0.2533	-0.0038	0.0327	0.2388	0.0152	0.0293	0.1296	-0.0082	0.1417	-9.362	-20.623	-32.454
16	0.0132	0.0069	0.0127	0.0262	0.0939	0.0892	0.0526	-0.0127	0.2396	0.1639	-0.0981	0.0711	-0.4578	0.0818	0.0004	0.2162	0.0237	0.0023	0.2297	0.0069	0.2434	-7.357	-10.645	-21.791

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 1:10 )	A	1 - 10
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 11:17 )	A	11 - 17
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 18:37 )	A	18 - 37
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 38:43 )	A	38 - 43
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 44:64 )	A	44 - 64
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 65:87 )	A	65 - 87
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 88:110 )	A	88 - 110
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 111:135 )	A	111 - 135
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 2:13 )	B	2 - 13
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 14:22 )	B	14 - 22
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 23:63 )	B	23 - 63
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 64:71 )	B	64 - 71
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 72:86 )	B	72 - 86
14	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 87:108 )	B	87 - 108
15	X-RAY DIFFRACTION	15	( CHAIN B AND RESID 109:128 )	B	109 - 128
16	X-RAY DIFFRACTION	16	( CHAIN B AND RESID 129:135 )	B	129 - 135

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