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- PDB-7n4o: Crystal structure of R20A human Galectin-7 mutant -

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Basic information

Entry
Database: PDB / ID: 7n4o
TitleCrystal structure of R20A human Galectin-7 mutant
Components(Galectin-7) x 2
KeywordsSUGAR BINDING PROTEIN / human galectin-7 / dimer interface mutant
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: 2.05 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 R20A human Galectin-7 mutant
Authors: Pham, N.T.H. / Calmettes, C. / Doucet, N.
History
DepositionJun 4, 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
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)30,2067
Polymers29,7752
Non-polymers4305
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.430, 64.640, 71.810
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: 14879.734 Da / Num. of mol.: 1 / Mutation: 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: Protein Galectin-7 / / Gal-7 / HKL-14 / PI7 / p53-induced gene 1 protein


Mass: 14895.734 Da / Num. of mol.: 1 / Mutation: 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
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
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: 2.04 Å3/Da / Density % sol: 40.93 %
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 , 20% 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: 1.89→48.04 Å / Num. obs: 20513 / % possible obs: 100 % / Redundancy: 7.241 % / Biso Wilson estimate: 31.73 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.134 / Rrim(I) all: 0.145 / Χ2: 1.012 / Net I/σ(I): 12.87 / Num. measured all: 148532 / Scaling rejects: 20
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.89-27.2972.4390.8822884313731360.3242.627100
2-2.137.3131.3021.6921493293929390.5991.401100
2.13-2.277.2740.7782.8617749244024400.8120.838100
2.27-2.447.3110.5234.2416728229022880.9160.56399.9
2.44-2.637.3210.3346.6114027191619160.9650.36100
2.63-2.857.2820.2379.3111812162216220.9810.255100
2.85-3.127.2450.13615.210426143914390.9930.147100
3.12-3.447.2330.07525.138455116911690.9980.081100
3.44-3.847.2020.04936.169799699690.9990.053100
3.84-4.347.1770.03942.6755417727720.9990.042100
4.34-57.0810.02753.11434861461410.029100
5-48.046.6910.02749.780901213120910.02999.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.89 Å48.04 Å
Translation5.89 Å48.04 Å

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.7.12phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1bkz

1bkz


Resolution: 2.05→48.04 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2521 1575 9.75 %
Rwork0.185 14576 -
obs0.1915 16151 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.67 Å2 / Biso mean: 41.5153 Å2 / Biso min: 17.27 Å2
Refinement stepCycle: final / Resolution: 2.05→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2105 0 66 143 2314
Biso mean--56.83 43.4 -
Num. residues----270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062246
X-RAY DIFFRACTIONf_angle_d0.7493049
X-RAY DIFFRACTIONf_chiral_restr0.055320
X-RAY DIFFRACTIONf_plane_restr14.888417
X-RAY DIFFRACTIONf_dihedral_angle_d10.569850
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
2.05-2.120.30121400.255412971437
2.12-2.190.31341400.239512921432
2.19-2.280.30821400.233413021442
2.28-2.380.30581410.20513041445
2.38-2.510.23451420.199113051447
2.51-2.670.24581420.197213191461
2.67-2.870.28841420.20313121454
2.87-3.160.25961430.188213281471
3.16-3.620.2571440.163713351479
3.62-4.560.19451470.146213491496
4.56-48.040.25361540.187914331587
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)
11.4399-0.28990.35860.67670.10681.60340.0433-0.07690.0133-0.01520.01250.07520.1353-0.06500.2655-0.00670.01750.18920.00430.2188-8.5139-21.1313-25.9576
20.5084-0.5988-0.76180.68410.82762.4749-0.05350.2073-0.1478-0.1381-0.27610.75410.0858-0.5536-0.07720.3375-0.03580.00640.24770.03120.3820.2889-30.7296-4.7678
30.56130.04320.07660.5049-0.48120.4775-0.0847-0.04330.14710.3562-0.23560.05760.6626-0.5545-0.08880.1919-0.04380.01840.2780.01580.2025-0.9174-24.2303-13.8684
40.84540.2144-0.60720.32980.23280.94240.0288-0.0490.08050.04370.0033-0.17680.03610.0186-00.19120.0006-0.02480.2389-0.00550.21989.8905-20.3159-2.2882
50.4863-0.5203-0.02731.2422-0.44380.57030.25940.1434-1.04620.12-0.3413-0.0210.2070.08810.00660.250.0109-0.02560.3302-0.00620.425421.522-26.5957-7.7063
60.1140.1535-0.13350.2005-0.17350.11920.1657-0.02090.4908-0.090.0482-0.0562-0.1670.0514-00.2429-0.00370.00750.27090.020.27696.794-10.1139-4.3
70.5005-0.23150.50610.6392-0.24960.4922-0.01930.1630.0414-0.05710.01170.1083-0.1272-0.039-00.2216-0.02240.02130.2722-0.00210.23487.2087-18.9143-16.287
80.52840.46240.00290.95220.08240.0125-0.0250.03760.02430.00540.0257-0.03810.17050.0703-00.23620.00670.01410.26430.01540.21482.0108-26.4126-6.2346
90.0942-0.0335-0.0130.01180.00460.0013-0.22120.0691-0.0057-0.0777-0.23850.40180.3127-0.15610.00030.62480.1822-0.03610.92370.09230.721-20.2513-5.9946-33.1193
100.20120.3283-0.02670.535-0.03780.0020.44890.0895-0.24230.226-0.5397-0.54590.0746-0.2673-0.00420.2697-0.0023-0.01360.2577-0.03340.318-7.4175-9.9061-32.0574
110.40150.6380.64661.22241.031.03690.47530.01890.77471.18450.1406-0.48630.14340.00840.090.43490.1310.02420.3466-0.06130.41762.9951-17.058-30.5072
120.0892-0.01280.0070.3297-0.42290.50660.3726-0.00510.325-0.1688-0.1073-0.0194-0.09610.0160.00010.2210.00140.02340.33380.02260.2558-12.0886-14.9958-21.3678
130.2672-0.18070.23230.567-0.07510.4670.31370.7326-0.2032-0.2409-0.2430.0477-0.0823-0.6551-0.0050.33340.0504-0.03230.38340.00290.2802-16.4876-16.0684-32.6432
140.0125-0.16120.03773.95751.67313.0378-0.01550.41330.38020.39410.03780.15570.40750.0613-0.14210.2110.0522-0.02520.41930.08360.4108-11.6055-18.2893-41.9835
150.0929-0.08510.13320.16750.03220.38660.07010.5438-0.4366-0.3269-0.14660.39920.3163-0.46920.00930.2843-0.053-0.04090.2739-0.01430.3051-20.6677-23.5592-29.3149
160.4565-0.60570.41650.8724-0.53270.4557-0.0369-0.3881-0.2295-0.08710.4910.0660.7120.23190.05760.63450.0003-0.09960.4526-0.11990.3714-14.9801-27.5839-41.3214
170.1181-0.2128-0.06030.37830.02970.18130.0071-0.2924-00.00370.0120.28920.1018-0.4453-0.00030.3862-0.0375-0.00560.3740.01190.3085-21.174-21.8206-20.6641
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain B and resid 88:135)B88 - 135
2X-RAY DIFFRACTION2(chain A and resid 1:13)A1 - 13
3X-RAY DIFFRACTION3(chain A and resid 14:22)A14 - 22
4X-RAY DIFFRACTION4(chain A and resid 23:64)A23 - 64
5X-RAY DIFFRACTION5(chain A and resid 65:71)A65 - 71
6X-RAY DIFFRACTION6(chain A and resid 72:86)A72 - 86
7X-RAY DIFFRACTION7(chain A and resid 87:114)A87 - 114
8X-RAY DIFFRACTION8(chain A and resid 115:135)A115 - 135
9X-RAY DIFFRACTION9(chain B and resid 1:4)B1 - 4
10X-RAY DIFFRACTION10(chain B and resid 5:9)B5 - 9
11X-RAY DIFFRACTION11(chain B and resid 10:14)B10 - 14
12X-RAY DIFFRACTION12(chain B and resid 15:27)B15 - 27
13X-RAY DIFFRACTION13(chain B and resid 28:41)B28 - 41
14X-RAY DIFFRACTION14(chain B and resid 42:46)B42 - 46
15X-RAY DIFFRACTION15(chain B and resid 47:64)B47 - 64
16X-RAY DIFFRACTION16(chain B and resid 65:71)B65 - 71
17X-RAY DIFFRACTION17(chain B and resid 72:87)B72 - 87

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