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- PDB-6vtp: Crystal structure of G16C human Galectin-7 mutant -

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Basic information

Entry
Database: PDB / ID: 6vtp
TitleCrystal structure of G16C human Galectin-7 mutant
ComponentsGalectin-7
KeywordsSUGAR BINDING PROTEIN / Human Galectin-7 / G16C mutant / disulfide bond
Function / homology
Function and homology information


heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / carbohydrate binding / apoptotic process / extracellular space / extracellular exosome / nucleus / cytoplasm
Similarity search - Function
Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsPham, N.T.H. / Calmettes, C. / Doucet, N.
Funding support Canada, United States, 6items
OrganizationGrant numberCountry
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
Fonds de Recherche du Quebec - Sante (FRQS)Research Scholar Senior Career Award (281993) Canada
Fonds de Recherche du Quebec - Sante (FRQS)Junior 1 (251848) Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2017-06091 Canada
Fonds de Recherche du Quebec - Sante (FRQS)Doctoral Training scholarship (287239) Canada
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Perturbing dimer interactions and allosteric communication modulates the immunosuppressive activity of human galectin-7.
Authors: Pham, N.T.H. / Letourneau, M. / Fortier, M. / Begin, G. / Al-Abdul-Wahid, M.S. / Pucci, F. / Folch, B. / Rooman, M. / Chatenet, D. / St-Pierre, Y. / Lague, P. / Calmettes, C. / Doucet, N.
History
DepositionFeb 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 24, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 11, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galectin-7
B: Galectin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2084
Polymers30,0242
Non-polymers1842
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-1 kcal/mol
Surface area12200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.600, 67.150, 71.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 19 or resid 22 through 29 or resid 31 through 135))
21(chain B and (resid 4 through 19 or resid 22 through 29 or resid 31 through 135))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLEULEU(chain A and (resid 4 through 19 or resid 22 through 29 or resid 31 through 135))AA4 - 194 - 19
12ARGARGALAALA(chain A and (resid 4 through 19 or resid 22 through 29 or resid 31 through 135))AA22 - 2922 - 29
13ARGARGPHEPHE(chain A and (resid 4 through 19 or resid 22 through 29 or resid 31 through 135))AA31 - 13531 - 135
21PROPROLEULEU(chain B and (resid 4 through 19 or resid 22 through 29 or resid 31 through 135))BB4 - 194 - 19
22ARGARGALAALA(chain B and (resid 4 through 19 or resid 22 through 29 or resid 31 through 135))BB22 - 2922 - 29
23ARGARGPHEPHE(chain B and (resid 4 through 19 or resid 22 through 29 or resid 31 through 135))BB31 - 13531 - 135

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Components

#1: Protein Galectin-7 / Gal-7 / HKL-14 / PI7 / p53-induced gene 1 protein


Mass: 15011.941 Da / Num. of mol.: 2 / Mutation: G16C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS7, PIG1, LGALS7B / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P47929
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.93 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Sodium chloride, 0.1M Tris pH 8, 20 % PEG 3350, 15 % Glycerol
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.0332 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 19, 2019 / Details: 16 tiled fiber-optic tapers
RadiationMonochromator: KOHZU double crystal mochochromator (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.3→49.08 Å / Num. obs: 11900 / % possible obs: 98.97 % / Redundancy: 9.68 % / Biso Wilson estimate: 52.768 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.151 / Rrim(I) all: 0.159 / Net I/σ(I): 14.5 / Num. measured all: 115145
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 10.01 % / Rmerge(I) obs: 2.416 / Mean I/σ(I) obs: 1.2 / Num. measured obs: 11553 / Num. unique obs: 1154 / CC1/2: 0.569 / Rrim(I) all: 2.545 / % possible all: 98.13

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å49.08 Å
Translation2.5 Å49.08 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.7.12phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1bkz

1bkz


Resolution: 2.3→49.08 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2606 1189 10.01 %
Rwork0.214 10687 -
obs0.2189 11876 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.19 Å2 / Biso mean: 65.2367 Å2 / Biso min: 28.01 Å2
Refinement stepCycle: final / Resolution: 2.3→49.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2099 0 12 44 2155
Biso mean--48.07 49.48 -
Num. residues----267
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1194X-RAY DIFFRACTION11.301TORSIONAL
12B1194X-RAY DIFFRACTION11.301TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.40.34551420.37251292143498
2.4-2.530.3281460.33751290143698
2.53-2.690.33911410.28871325146698
2.69-2.90.31451470.27931311145899
2.9-3.190.30641510.23521332148399
3.19-3.650.24611540.20691328148299
3.65-4.60.21961480.17081363151199
4.6-49.080.23881600.1781446160699
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
13.3551-1.87370.80576.2709-2.05225.99810.362-0.24720.27670.6138-0.39190.5052-0.37681.31090.15380.4893-0.15480.02860.4534-0.07850.5904-0.459-2.087-0.326
23.7026-1.14650.70092.2171-0.21692.1345-0.1470.29250.21120.3738-0.2607-0.4002-0.34020.08060.32240.26290.0087-0.00410.34260.02390.334-3.031-11.447-4.872
34.6882-1.3357-0.55272.2458-0.87522.61950.0942-0.31150.73170.04370.2272-0.0398-0.196-0.0808-0.26440.3341-0.04350.05910.332-0.02830.3916-12.584-10.418-2.51
43.7205-1.12060.04660.9434-0.37792.58030.08040.06910.1140.0039-0.024-0.0390.0012-0.3935-0.02520.3797-0.0254-0.00180.42380.03670.4295-11.997-15.288-5.342
54.9166-1.5919-0.64534.41130.47310.54460.08361.65140.8275-1.0163-0.3038-0.0671-0.1468-0.27730.31120.5362-0.0820.05210.63970.19110.5235-6.447-7.951-16.218
62.1029-0.86670.64867.4822-0.2229.4665-0.63581.05210.051-0.45460.02820.43240.43-0.33370.70260.4161-0.0557-0.00280.35710.02850.3551-4.072-18.535-14.943
73.531-0.5027-2.2035.3627-0.79982.10780.03721.11190.6291-1.01020.32070.4577-0.314-0.627-0.08950.5258-0.0837-0.03860.55580.2140.5045-14.198-6.237-14.522
82.90320.4490.43812.3653-1.72992.49730.01330.22270.52690.2864-0.0983-0.3771-0.35090.22840.11760.3672-0.0012-0.00140.40150.090.4018-1.609-6.37-3.321
92.74260.7315-0.11023.9232-2.86922.37440.645-0.548-0.1875-0.6264-0.4306-1.36740.6663-1.1327-0.05861.123-0.07350.2270.72320.06991.205511.04-20.414-32.025
107.74541.15452.9181.2156-1.45485.4384-1.69930.7646-1.7326-1.34741.37132.40210.4049-1.31590.49220.9838-0.2871-0.05330.97830.14480.8672-2.085-12.045-31.699
117.73290.65182.8151.66722.77085.01961.0864-0.5768-0.7462-0.50860.20210.4334-0.230.73180.27790.5892-0.21610.1640.86720.29640.61234.227-12.62-20.828
121.1221-0.09710.14250.006-0.01390.0165-0.010.1035-0.3917-1.1449-0.4852-1.20930.75720.75580.10370.81240.35170.46160.89260.5421.170819.153-19.374-18.485
130.7018-1.2984-0.85493.64451.33861.0702-0.33720.36-0.9693-1.1506-0.1404-1.27011.14440.52150.22120.87710.0740.45580.78240.22540.950616.993-12.459-29.753
143.3897-0.25621.01455.5871-0.15774.10010.14511.2888-0.4721-1.1151-0.2361-1.6510.86761.81680.07930.860.10550.36980.83760.13970.849217.212-7.59-30.75
152.836-0.3962-1.72295.56921.99814.66050.31090.90010.2922-1.6850.51051.3590.40040.2324-0.22481.5161-0.17630.38330.6563-0.06040.713312.856-2.084-40.838
162.38240.318-0.63112.3746-0.33881.254-0.5483-0.4685-0.3391-0.2681-0.1804-1.39050.19760.95810.20150.63850.1420.15560.83140.19670.796719.494-7.27-21.831
173.83220.8541-0.83233.82240.58783.2194-0.1765-0.44210.28630.3497-0.0178-0.054-0.45620.44430.02740.41980.02630.05150.4380.1190.36076.541-4.345-20.002
183.47450.56531.75223.2070.46064.4973-0.84570.45830.6906-0.36320.65460.269-0.30610.2289-0.04860.67760.0579-0.01050.57720.17830.5257.734-0.245-27.788
199.1212-6.75261.9335.2517-2.55485.48370.26330.4627-0.3192-0.6016-1.45820.30110.7630.99931.01521.2938-0.0280.23570.52770.08340.92817.42-13.55-33.185
206.2126-0.1443-1.02013.1752-0.30912.54560.29620.073-0.2853-0.6016-0.387-1.07951.02310.6440.22670.8984-0.01880.22320.64560.03610.633310.61-19.178-22.839
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:12 )A1 - 12
2X-RAY DIFFRACTION2( CHAIN A AND RESID 13:37 )A13 - 37
3X-RAY DIFFRACTION3( CHAIN A AND RESID 38:62 )A38 - 62
4X-RAY DIFFRACTION4( CHAIN A AND RESID 63:87 )A63 - 87
5X-RAY DIFFRACTION5( CHAIN A AND RESID 88:98 )A88 - 98
6X-RAY DIFFRACTION6( CHAIN A AND RESID 99:106 )A99 - 106
7X-RAY DIFFRACTION7( CHAIN A AND RESID 107:115 )A107 - 115
8X-RAY DIFFRACTION8( CHAIN A AND RESID 116:135 )A116 - 135
9X-RAY DIFFRACTION9( CHAIN B AND RESID 4:6 )B4 - 6
10X-RAY DIFFRACTION10( CHAIN B AND RESID 7:15 )B7 - 15
11X-RAY DIFFRACTION11( CHAIN B AND RESID 16:21 )B16 - 21
12X-RAY DIFFRACTION12( CHAIN B AND RESID 22:27 )B22 - 27
13X-RAY DIFFRACTION13( CHAIN B AND RESID 28:39 )B28 - 39
14X-RAY DIFFRACTION14( CHAIN B AND RESID 40:62 )B40 - 62
15X-RAY DIFFRACTION15( CHAIN B AND RESID 63:68 )B63 - 68
16X-RAY DIFFRACTION16( CHAIN B AND RESID 69:88 )B69 - 88
17X-RAY DIFFRACTION17( CHAIN B AND RESID 89:104 )B89 - 104
18X-RAY DIFFRACTION18( CHAIN B AND RESID 105:117 )B105 - 117
19X-RAY DIFFRACTION19( CHAIN B AND RESID 118:124 )B118 - 124
20X-RAY DIFFRACTION20( CHAIN B AND RESID 125:135 )B125 - 135

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