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- PDB-7n6c: Crystal structure of R22A human Galectin-7 mutant -

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Basic information

Entry
Database: PDB / ID: 7n6c
TitleCrystal structure of R22A human Galectin-7 mutant
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 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. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Galectin-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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
Other governmentFonds de Recherche du Quebec - Sante (FRQ-S) - Research Scholar Senior Career Award (281993) Canada
Other governmentFonds de Recherche du Quebec - Sante (FRQ-S) - Junior 1 (251848) Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2017-06091 Canada
Other governmentFonds de Recherche du Quebec - Sante (FRQ-S) - Doctoral Training scholarship (287239) Canada
CitationJournal: To Be Published
Title: Crystal structure of R20A human Galectin-7 mutant
Authors: Pham, N.T.H. / Calmettes, C. / Doucet, N.
History
DepositionJun 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 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)30,57412
Polymers29,7592
Non-polymers81510
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.350, 64.890, 71.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 14879.734 Da / Num. of mol.: 2 / Mutation: 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

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Non-polymers , 5 types, 127 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.09 Å3/Da / Density % sol: 41.18 %
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, 17.5% 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.05→48.19 Å / Num. obs: 16194 / % possible obs: 99.9 % / Redundancy: 10.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.12 / Rrim(I) all: 0.127 / Net I/σ(I): 12.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible allRpim(I) all
2.05-2.1210.21.3711.815700.6851.44399.8
2.12-2.2110.20.982.515870.7871.03199.90.318
2.21-2.3110.20.6773.715970.8980.71399.90.22
2.31-2.4310.20.5244.715930.9280.552100
2.43-2.5810.20.4026.216000.9590.4231000.13
2.58-2.7810.20.2858.516080.9790.31000.093
2.78-3.06130.1731316090.9920.18299.90.057
3.06-3.51100.120.516360.9970.1061000.033
3.51-4.429.90.06529.716540.9980.0681000.021
4.42-48.199.40.0534.317400.9980.05299.80.017

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.9 Å48.17 Å
Translation5.9 Å48.17 Å

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
XSCALEdata scaling
PHASER2.7.12phasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1bkz

1bkz


Resolution: 2.1→48.17 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 1510 10 %
Rwork0.1972 13591 -
obs0.201 15101 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 192.77 Å2 / Biso mean: 48.8005 Å2 / Biso min: 15.65 Å2
Refinement stepCycle: final / Resolution: 2.1→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 0 129 117 2344
Biso mean--69.01 42.69 -
Num. residues----269
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1-2.170.27021360.24412111347
2.17-2.250.33431340.24812101344
2.25-2.340.30181340.248312111345
2.34-2.440.29521350.232812151350
2.44-2.570.29541370.234112231360
2.57-2.730.27281340.223812121346
2.73-2.940.26381360.226312261362
2.94-3.240.27631370.20712391376
3.24-3.710.2161390.174812451384
3.71-4.670.17251410.150512721413
4.67-48.170.20991470.19513271474
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)
10.5777-0.05150.37640.0048-0.01332.06410.09230.07580.210.24730.44051.294-0.5463-0.9445-0.43690.64010.0464-0.14340.45560.33351.3416-1.2372-24.49124.9502
23.5225-1.5441-2.34117.03444.17283.1615-0.00230.0078-0.53530.3583-0.10270.67390.3982-0.08530.09190.3833-0.0461-0.10630.26910.0320.47521.063-33.2844-8.51
33.8002-1.1769-2.70942.83383.5999.1142-0.1380.3147-0.57340.3267-0.10670.26640.6269-0.41160.27440.279-0.0590.00610.29780.02170.2738-0.1633-25.1644-15.1494
41.4747-0.4128-0.33811.76830.45461.1275-0.0845-0.00060.07370.04370.203-0.16170.13280.0423-0.09110.2145-0.0175-0.02220.25870.02720.24229.8388-20.4464-2.3494
53.811-0.9141-0.39811.4597-0.67691.50880.0920.1287-0.1853-0.1424-0.01040.2181-0.14460.0639-0.07760.1975-0.0543-0.03410.24530.02410.300510.9402-15.5482-5.5201
62.5698-1.1337-0.46673.26740.78962.50550.00650.3940.1986-0.44540.0965-0.02660.00330.0908-0.08540.24-0.054-0.00740.3470.03790.19877.7782-19.2609-16.5849
70.72630.32-0.24622.420.93471.7377-0.10460.0559-0.1915-0.05720.01380.13320.301-0.05980.08920.2354-0.02530.00810.24360.03620.27261.7934-26.7036-6.0802
82.8452-0.6704-1.11395.6596-0.01634.81180.20410.26070.4416-0.1027-0.188-0.0801-0.1569-0.6688-0.06310.4860.1147-0.07420.53250.00060.4158-7.2117-11.0289-32.271
94.4963-2.4373-2.10865.04063.89683.3950.3953-0.27080.5428-0.66250.4827-0.3863-0.15641.2129-0.80670.4283-0.03940.03320.3684-0.05630.2723-1.4829-18.9637-23.9375
103.0237-0.347-0.36591.55190.26893.07220.28830.29920.2328-0.4174-0.02570.34660.0026-0.6296-0.18740.43850.012-0.11550.35680.01210.4487-16.5062-16.6874-31.0043
114.1183-1.8638-0.5282.90550.88464.44410.07010.3125-0.6769-0.37820.22720.57460.7705-1.3793-0.33210.5747-0.1789-0.18560.5330.08690.6363-21.1818-24.7707-30.2569
123.82053.0656-2.29476.1076-4.84123.8516-0.01030.0472-0.9674-0.4179-0.2288-0.38320.76990.42040.33820.99270.0519-0.20460.485-0.14870.7365-15.859-27.911-40.9047
132.0484-1.3847-0.01923.5331.71953.58270.2196-0.8275-0.8882-0.30490.14590.9732-0.2203-0.7234-0.4230.5033-0.0994-0.08020.58670.22590.6475-21.2158-21.7272-20.5881
144.2323-0.57080.02292.81750.07753.07630.0784-0.1883-0.809-0.2085-0.16240.48970.8048-0.10690.08830.4697-0.026-0.06290.276-0.00740.3842-8.1105-27.0144-24.6903
153.59410.08680.47761.9488-1.25591.07410.30080.11580.1593-0.2713-0.07310.08030.1766-0.1906-0.22610.4836-0.003-0.01810.30830.03240.3654-9.4318-13.5749-28.6881
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 5:13)A5 - 13
3X-RAY DIFFRACTION3(chain A and resid 14:21)A14 - 21
4X-RAY DIFFRACTION4(chain A and resid 22:64)A22 - 64
5X-RAY DIFFRACTION5(chain A and resid 65:87)A65 - 87
6X-RAY DIFFRACTION6(chain A and resid 88:114)A88 - 114
7X-RAY DIFFRACTION7(chain A and resid 115:135)A115 - 135
8X-RAY DIFFRACTION8(chain B and resid 2:13)B2 - 13
9X-RAY DIFFRACTION9(chain B and resid 14:20)B14 - 20
10X-RAY DIFFRACTION10(chain B and resid 21:52)B21 - 52
11X-RAY DIFFRACTION11(chain B and resid 53:65)B53 - 65
12X-RAY DIFFRACTION12(chain B and resid 66:71)B66 - 71
13X-RAY DIFFRACTION13(chain B and resid 72:87)B72 - 87
14X-RAY DIFFRACTION14(chain B and resid 88:115)B88 - 115
15X-RAY DIFFRACTION15(chain B and resid 116:135)B116 - 135

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