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- PDB-7tro: Crystal structure of R14A-R20A human Galectin-7 mutant in presenc... -

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Basic information

Entry
Database: PDB / ID: 7tro
TitleCrystal structure of R14A-R20A human Galectin-7 mutant in presence of lactose
ComponentsGalectin-7
KeywordsSUGAR 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 / 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. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-lactose / Galectin-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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)FRQ-S Research Scholar Senior Career Award (281993) Canada
Fonds de Recherche du Quebec - Sante (FRQS)FRQ-S Junior 1 (251848) Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2017-06091 Canada
Fonds de Recherche du Quebec - Sante (FRQS)FRQ-S Doctoral Training scholarship (287239) Canada
CitationJournal: To Be Published
Title: Crystal structure of R14A-R20A human Galectin-7 mutant in presence of lactose
Authors: Pham, N.T.H. / Calmettes, C. / Doucet, N.
History
DepositionJan 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)30,1145
Polymers29,5872
Non-polymers5273
Water4,828268
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.970, 66.160, 70.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14793.617 Da / Num. of mol.: 2 / Mutation: R14A, R20A
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: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.13 Å3/Da / Density % sol: 42.21 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M NaCl,0.1 M Tris pH 8, 20 % PEG 6000, 5% Glycerol, 7.5 mM Lactose
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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→48.28 Å / Num. obs: 23994 / % possible obs: 99.8 % / Redundancy: 9.3 % / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.018 / Rrim(I) all: 0.055 / Net I/σ(I): 24.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.866.60.7932.223670.770.3280.86199.8
1.86-1.949.10.5394.323440.9410.1860.57199.4
1.94-2.039.80.3237.423560.9770.1070.341100
2.03-2.139.80.20311.623930.9890.0670.214100
2.13-2.279.70.14616.223410.9940.0490.15498.6
2.27-2.449.80.10720.723780.9970.0350.11299.9
2.44-2.699.80.07428.524100.9980.0250.079100
2.69-3.089.70.0538.724100.9990.0170.53100
3.08-3.889.60.03553.724450.9990.0120.037100
3.88-48.289.20.02859.4255010.010.0399.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.64 Å48.26 Å
Translation1.64 Å48.26 Å

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.7.12phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4gal

4gal


Resolution: 1.8→35.97 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 1558 6.5 %
Rwork0.175 22426 -
obs0.178 23984 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.6 Å2 / Biso mean: 36.5192 Å2 / Biso min: 14.53 Å2
Refinement stepCycle: final / Resolution: 1.8→35.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2071 0 75 268 2414
Biso mean--60.67 39.05 -
Num. residues----267
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.860.3771350.325420262161100
1.86-1.920.35941440.275919802124100
1.92-20.2681390.216319932132100
2-2.090.23051360.19520252161100
2.09-2.20.24871330.187120322165100
2.2-2.340.27851460.19881993213998
2.34-2.520.22531400.178620252165100
2.52-2.780.24671440.187220362180100
2.78-3.180.22451420.179220692211100
3.18-40.16071410.143120672208100
4-35.970.20131580.152821802338100
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)
10.0313-0.01280.02230.02090.00150.01460.30120.0174-0.191-0.22340.1142-0.01310.04370.6613-0.00020.6517-0.11640.08830.603-0.10860.680428.3273-9.28856.0249
20.1568-0.29240.0370.067-0.0740.0799-0.03130.14170.25150.047-0.1013-0.2354-0.12060.0944-0.00110.2643-0.0299-0.03510.254-0.00380.264325.8626-1.1789-8.7834
30.4921-0.06240.350.6705-0.23070.61040.0259-0.0618-0.03410.0463-0.0070.0403-0.0903-0.019-00.20190.01570.02190.2291-00.191717.3271-11.8321-1.8386
40.71480.3136-0.29160.122-0.06690.71260.13420.1133-0.0507-0.0986-0.06440.0499-0.0734-0.021700.2122-0.00130.01090.2136-0.01330.209515.8121-16.2148-5.4447
50.12320.0076-0.16640.14730.10310.18070.02170.23720.0266-0.26080.01970.12760.0811-0.014400.17720.00050.00030.23170.01140.158921.8337-10.176-15.7778
60.09270.25460.0530.40440.16460.2627-0.08990.24380.14950.06470.0029-0.0504-0.1364-0.086700.1925-0.0133-0.00640.25450.00480.190416.4684-12.8404-15.6435
70.2317-0.2314-0.00510.00780.02410.0908-0.0856-0.15220.14980.13460.0781-0.163-0.2248-0.054800.26030.01310.00390.2222-0.00150.241220.0908-3.7436-4.3251
80.1510.10870.0352-0.012-0.06380.0781-0.03110.04020.12130.0911-0.185-0.3589-0.3010.3907-00.2361-0.012-0.00530.25580.01410.267732.2783-7.9578-5.9352
90.04540.05210.01610.05410.03320.0756-0.04670.3384-0.07670.01490.1753-0.2716-0.09060.5863-00.54540.00120.02920.4512-0.05650.472532.8191-18.3395-32.5166
100.0378-0.0639-0.04830.09230.1210.0539-0.12630.2058-0.3977-0.069-0.0006-0.10330.12190.3284-0.00010.2868-0.00580.03560.2656-0.00320.27527.8491-10.4075-25.3163
110.2810.1096-0.17920.2603-0.15120.77450.0714-0.0872-0.4061-0.335-0.0115-0.29180.35890.181-0.0530.30340.08080.06880.30080.00090.38544.7819-14.7378-26.5721
120.02870.00050.04170.0439-0.01840.0351-0.1391-0.0926-0.23380.01320.14150.039-0.1656-0.0829-0.00060.4871-0.00710.04140.4272-0.05820.393835.283-14.2885-42.6361
130.0810.0924-0.15260.2311-0.19060.263-0.14660.0034-0.1334-0.304-0.0127-0.50360.06350.2936-0.00080.30690.03070.06540.32690.03020.390645.6863-6.0969-28.9059
140.0476-0.00430.00580.0140.00950.01960.01490.46-0.0354-0.1850.12660.42820.3324-0.4642-00.6676-0.02910.16490.42440.01950.462539.74-2.5695-41.9338
150.15550.2339-0.19570.88050.27850.5516-0.0499-0.19610.06620.01210.0061-0.34840.10480.2601-0.00010.27330.04640.03980.3430.04840.356842.8925-6.1716-22.3074
160.5724-0.2258-0.29310.73950.18680.2360.0235-0.076-0.1226-0.185-0.0309-0.12850.2102-0.1100.28110.01140.00560.2430.00540.264635.1622-4.39-26.2977
170.55180.42570.63410.21320.48331.06320.16470.0419-0.27580.3532-0.103-0.47860.50260.03310.02350.37710.10380.03240.24330.02890.439238.8566-19.1403-23.3428
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:4)A1 - 4
2X-RAY DIFFRACTION2(chain A and resid 5:21)A5 - 21
3X-RAY DIFFRACTION3(chain A and resid 22:64)A22 - 64
4X-RAY DIFFRACTION4(chain A and resid 65:87)A65 - 87
5X-RAY DIFFRACTION5(chain A and resid 88:102)A88 - 102
6X-RAY DIFFRACTION6(chain A and resid 103:112)A103 - 112
7X-RAY DIFFRACTION7(chain A and resid 113:128)A113 - 128
8X-RAY DIFFRACTION8(chain A and resid 129:135)A129 - 135
9X-RAY DIFFRACTION9(chain B and resid 4:10)B4 - 10
10X-RAY DIFFRACTION10(chain B and resid 11:21)B11 - 21
11X-RAY DIFFRACTION11(chain B and resid 22:39)B22 - 39
12X-RAY DIFFRACTION12(chain B and resid 40:43)B40 - 43
13X-RAY DIFFRACTION13(chain B and resid 44:63)B44 - 63
14X-RAY DIFFRACTION14(chain B and resid 64:68)B64 - 68
15X-RAY DIFFRACTION15(chain B and resid 69:96)B69 - 96
16X-RAY DIFFRACTION16(chain B and resid 97:123)B97 - 123
17X-RAY DIFFRACTION17(chain B and resid 124:135)B124 - 135

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