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- PDB-7tkz: Crystal structure of D94A human Galectin-7 mutant in presence of ... -

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Basic information

Entry
Database: PDB / ID: 7tkz
TitleCrystal structure of D94A 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 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
alpha-lactose / DI(HYDROXYETHYL)ETHER / Galectin-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.83 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
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2017-06091 Canada
Fonds de Recherche du Quebec - Sante (FRQS)FRQS Junior 1 (251848) Canada
Fonds de Recherche du Quebec - Sante (FRQS)FRQ-S Doctoral Training scholarship (287239) Canada
CitationJournal: To Be Published
Title: Crystal structure of D94A human Galectin-7 mutant in presence of lactose
Authors: Pham, N.T.H. / Calmettes, C. / Doucet, N.
History
DepositionJan 17, 2022Deposition 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,7286
Polymers29,8762
Non-polymers8534
Water4,900272
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.230, 76.400, 111.090
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: 14937.840 Da / Num. of mol.: 2 / Mutation: D94A
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)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-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: isolated from a genetically manipulated source
Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.87 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M NaCl, 0.1 M Tris pH 8.0, 20 % PEG 6000, 15% 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: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.83→44.94 Å / Num. obs: 23542 / % possible obs: 99.9 % / Redundancy: 6.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.107 / Rrim(I) all: 0.081 / Net I/σ(I): 6.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.83-1.96.30.2486.823440.980.1070.27199.9
1.9-1.976.20.1749.322880.9860.0770.19199.9
1.97-2.065.90.13111.722930.990.0590.14499.5
2.06-2.176.10.10914.323380.9930.0480.1299.9
2.17-2.316.30.09416.323110.9950.0410.10399.9
2.31-2.486.40.09317.823230.9950.040.101100
2.48-2.736.20.08619.823720.9950.0380.09499.9
2.73-3.136.50.07923.423470.9960.0340.086100
3.13-3.946.30.06327.523960.9960.0280.06999.9
3.94-44.9460.05428.325300.9970.0240.05999.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.54 Å44.93 Å
Translation1.54 Å44.93 Å

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.7.12phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4gal

4gal


Resolution: 1.83→44.93 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2248 1235 5.25 %
Rwork0.1663 22293 -
obs0.1693 23528 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.99 Å2 / Biso mean: 25.0179 Å2 / Biso min: 6.91 Å2
Refinement stepCycle: final / Resolution: 1.83→44.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2083 0 117 272 2472
Biso mean--37.21 33.53 -
Num. residues----266
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.83-1.90.25681350.252624362571
1.9-1.990.25341350.183424272562
1.99-2.090.22441330.174124202553
2.09-2.230.23891360.171324482584
2.23-2.40.2811360.170724402576
2.4-2.640.231370.172224792616
2.64-3.020.21351370.168224922629
3.02-3.810.21851400.137125132653
3.81-44.930.1941460.161926382784
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)
10.1214-0.01680.02080.0148-0.01840.03250.05260.1381-0.0087-0.08910.07850.03040.0076-0.19860.00750.1479-0.0068-0.01540.1538-0.01470.1958-13.926-0.814-28.393
20.0327-0.0434-0.01270.09090.04940.0352-0.0193-0.03230.0206-0.0401-0.13250.2106-0.0022-0.1863-0.13830.2231-0.0077-0.05570.2712-0.16920.2449-12.43813.091-20.08
30.14730.0328-0.00880.1092-0.12930.13630.00250.0338-0.05770.0587-0.01790.07590.089-0.11290.04870.11120.00220.00340.0874-0.01610.125-4.972-2.627-26.272
40.20880.14830.07110.15950.08830.1379-0.02150.0783-0.0687-0.13690.0439-0.0740.06670.00810.03920.09670.00530.01180.08060.00630.09771.4931.637-32.648
50.02260.0063-0.00550.03320.00270.00110.02510.00340.3188-0.2026-0.0424-0.079-0.25460.02770.01590.18740.0034-0.00940.12550.01150.13721.44811.578-37.767
60.08410.0565-0.10440.0757-0.14990.2536-0.0047-0.0068-0.07130.00260.0011-0.04320.0290.0658-0.00710.10720.00160.00070.076-0.00680.11133.079-2.063-22.883
70.0897-0.1006-0.07230.08370.08110.0896-0.0713-0.03960.06110.08480.0891-0.0633-0.04530.03150.05330.12280.00320.00850.0790.00710.11561.5857.548-22.352
80.0487-0.004-0.02320.01850.01690.0211-0.14640.09990.06570.0453-0.06110.0438-0.09530.0165-0.02310.08920.0045-0.02280.09960.00780.1893-11.1074.287-29.102
90.1440.01050.0510.01140.00880.0283-0.0196-0.0714-0.17360.032-0.12790.2437-0.00830.02570.00980.1292-0.02120.00040.1054-0.02280.1573-9.149-6.105-22.902
100.4734-0.7558-0.08494.93490.9060.51230.07490.0208-0.0064-0.01320.0454-0.0140.02270.04080.01310.33540.11930.06080.3530.17060.44294.339-5.2966.661
110.0274-0.02740.01040.0236-0.00860.0023-0.1016-0.02730.1623-0.005-0.1217-0.0993-0.05260.113600.1677-0.0032-0.01810.21610.01310.21276.1937.86-1.034
120.03870.00870.07740.00430.00520.0925-0.0104-0.0952-0.017-0.0005-0.05-0.10210.05910.0413-00.1236-0.00520.00910.076-0.00290.1177-1.2092.432-8.267
130.1172-0.0088-0.05630.2405-0.2470.2498-0.0519-0.1954-0.0012-0.01230.0312-0.01470.03890.0469-0.0180.12580.00680.01160.1629-0.00140.1313-7.1762.2016.87
140.0057-0.0191-0.01340.17790.05220.0327-0.0506-0.08960.12880.1455-0.0110.0137-0.077-0.05-0.12260.24990.0077-0.00260.3921-0.22410.367-5.9816.18911.077
150.04770.2081-0.09480.9074-0.41260.18710.0835-0.10670.1616-0.08720.1913-0.0124-0.0366-0.01560.12380.21770.01420.02390.2405-0.08290.1506-12.64912.85110.079
160.0973-0.0973-0.0650.08440.08450.1779-0.0213-0.0362-0.07050.02680.0070.09070.0498-0.084100.1218-0.00030.00790.10260.01120.122-11.739-0.643-1.824
170.07170.1019-0.11260.1898-0.25020.30740.0144-0.11490.00960.01150.012-0.0719-0.06340.02260.00040.12180.0050.00540.1116-0.0170.1347-7.5658.274-2.696
180.05960.04140.06880.02830.04810.07290.0157-0.0951-0.1149-0.0199-0.1135-0.19230.02910.0535-00.15110.030.01210.20060.0450.1960.652-4.649-1.506
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:10 )A2 - 10
2X-RAY DIFFRACTION2( CHAIN A AND RESID 11:14 )A11 - 14
3X-RAY DIFFRACTION3( CHAIN A AND RESID 15:40 )A15 - 40
4X-RAY DIFFRACTION4( CHAIN A AND RESID 41:64 )A41 - 64
5X-RAY DIFFRACTION5( CHAIN A AND RESID 65:71 )A65 - 71
6X-RAY DIFFRACTION6( CHAIN A AND RESID 72:97 )A72 - 97
7X-RAY DIFFRACTION7( CHAIN A AND RESID 98:118 )A98 - 118
8X-RAY DIFFRACTION8( CHAIN A AND RESID 119:123 )A119 - 123
9X-RAY DIFFRACTION9( CHAIN A AND RESID 124:135 )A124 - 135
10X-RAY DIFFRACTION10( CHAIN B AND RESID 3:4 )B3 - 4
11X-RAY DIFFRACTION11( CHAIN B AND RESID 5:13 )B5 - 13
12X-RAY DIFFRACTION12( CHAIN B AND RESID 14:23 )B14 - 23
13X-RAY DIFFRACTION13( CHAIN B AND RESID 24:63 )B24 - 63
14X-RAY DIFFRACTION14( CHAIN B AND RESID 64:67 )B64 - 67
15X-RAY DIFFRACTION15( CHAIN B AND RESID 68:71 )B68 - 71
16X-RAY DIFFRACTION16( CHAIN B AND RESID 72:97 )B72 - 97
17X-RAY DIFFRACTION17( CHAIN B AND RESID 98:123 )B98 - 123
18X-RAY DIFFRACTION18( CHAIN B AND RESID 124:135 )B124 - 135

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