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- PDB-7trn: Crystal structure of R14A-R20A human Galectin-7 mutant -

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Basic information

Entry
Database: PDB / ID: 7trn
TitleCrystal structure of R14A-R20A human Galectin-7 mutant
ComponentsGalectin-7
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: 1.95 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
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
C: Galectin-7
D: Galectin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,25820
Polymers59,1744
Non-polymers1,08316
Water6,395355
1
A: Galectin-7
B: Galectin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,54616
Polymers29,5872
Non-polymers95914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Galectin-7
D: Galectin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7114
Polymers29,5872
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.050, 53.640, 69.370
Angle α, β, γ (deg.)87.460, 79.030, 84.840
Int Tables number1
Space group name H-MP1

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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.: 4 / 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: 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.22 Å3/Da / Density % sol: 44.48 %
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

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.95→42.61 Å / Num. obs: 31452 / % possible obs: 84.9 % / Redundancy: 2.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.039 / Rrim(I) all: 0.063 / Net I/σ(I): 16.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.95-2.022.50.2913.616590.8740.230.37244.8
2.02-2.12.50.2395.120890.9230.1890.30756.1
2.1-2.22.50.1686.631470.9420.1320.21585.4
2.2-2.312.70.1488.233390.9620.1160.18990
2.31-2.462.70.10610.335830.9760.0830.13697.1
2.46-2.652.60.08112.835860.9860.0630.10396.8
2.65-2.912.70.0616.335320.9910.0470.07695.4
2.91-3.32.70.0422.535980.9960.0310.05196.5
3.33-4.22.60.0329.934450.9970.0230.03893.5
4.2-42.612.70.02433.434740.9980.0190.03193.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.49 Å42.6 Å
Translation2.49 Å42.6 Å

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Processing

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

1bkz


Resolution: 1.95→41.46 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 25.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2254 1913 6.08 %
Rwork0.1949 29529 -
obs0.1968 31442 84.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.45 Å2 / Biso mean: 28.8405 Å2 / Biso min: 7.69 Å2
Refinement stepCycle: final / Resolution: 1.95→41.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4136 0 172 355 4663
Biso mean--48.65 32.12 -
Num. residues----533
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-20.3385830.30521070115343
2-2.050.3689770.27461280135752
2.05-2.110.27381050.2551494159961
2.11-2.180.25471250.2242133225886
2.18-2.260.28061550.24982207236288
2.26-2.350.24561520.21592363251596
2.35-2.460.24491610.20322410257197
2.46-2.590.2391390.20572450258997
2.59-2.750.26091590.20952328248795
2.75-2.960.25021600.19842411257197
2.96-3.260.23521490.19322393254296
3.26-3.730.18731550.16472342249795
3.73-4.70.161470.15132348249594
4.7-41.460.21581460.19142300244692
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)
11.97980.5574-3.14360.1759-0.93925.14590.2973-0.05220.33590.1168-0.0558-0.576-0.3660.0140.30230.37250.02780.07980.54680.43641.27815.314-26.79786.325
21.0159-0.3632-0.2560.85050.8131.31460.03540.0265-0.2624-0.2992-0.28120.3151-0.2027-0.32670.10920.18830.0689-0.03860.14150.00320.18376.191-28.40270.206
30.90230.18120.6691.5850.62051.44340.0255-0.0189-0.08550.053-0.08170.05590.0378-0.07190.02320.07240.00130.00390.07150.02380.119311.134-37.52181.37
40.90850.48460.1992.33090.4260.96240.02870.0601-0.0194-0.09230.0292-0.1889-0.05830.0588-0.05380.08280.00030.00320.08050.01790.102716.562-39.56880.436
51.48350.07820.16022.47631.29783.6010.02360.0864-0.0321-0.1988-0.0199-0.2396-0.0461-0.1741-0.07180.1543-0.00440.02540.09220.02120.114117.03-33.86368.165
63.38751.70981.09512.3050.59171.6465-0.07880.16610.0279-0.29310.043-0.13810.00460.0510.01250.18430.02590.01580.1550.00420.173118.931-38.96769.962
71.30960.47071.15981.07461.0854.25660.13150.1234-0.0337-0.028-0.11070.34930.4794-0.31660.02140.14630.0207-0.02320.13820.01780.19935.845-34.17575.155
80.74820.08142.19070.63480.7126.766-0.14490.03340.2683-0.3471-0.16810.1563-0.4353-0.37130.26970.21090.0038-0.03490.1320.01440.157110.992-22.2875.919
93.9043-0.7592.19662.9463-1.55726.14880.14340.04050.0239-0.09950.2581-0.22790.00850.25-0.30810.1119-0.0234-0.01820.1592-0.03720.25126.287-57.28293.907
102.0996-1.26550.54542.4997-2.31983.91240.0893-0.32140.07280.12070.2951-0.1031-0.0269-0.0434-0.27930.1333-0.0151-0.02310.0938-0.02930.149819.122-56.491103.2
111.4018-0.69680.65291.7811-0.04461.0714-0.00490.13010.069-0.1706-0.0999-0.0368-0.13440.07870.0950.1541-0.0089-0.00250.09150.01610.120114.929-60.10586.467
126.065.03292.83184.94444.01394.9373-0.20310.5518-0.1102-0.4998-0.08390.2458-0.3870.06250.23160.2009-0.0067-0.07270.2297-0.0790.453530.663-67.35592.64
130.73090.08820.55141.30910.3331.17120.11530.0137-0.0782-0.02370.02230.03010.0853-0.0288-0.13460.0853-0.0078-0.00080.08270.00060.121112.009-67.8290.224
146.6675-0.8-0.78676.1422.07992.746-0.04440.1674-0.70610.4604-0.279-0.69790.45830.11550.27180.18190.0067-0.02630.16990.01990.249523.079-76.5195.869
150.60090.2045-0.36091.6438-0.03830.67-0.0007-0.02430.02180.03350.04970.30110.0279-0.0499-0.00640.0635-0.017-0.0010.1015-0.0050.13948.436-62.69593.347
162.1523-0.5510.45851.63210.17391.4554-0.0065-0.16980.01010.2260.0417-0.00680.04440.0014-0.04620.1053-0.0353-0.0080.08620.0030.104513.831-63.683100.217
170.6685-0.24941.05390.1164-0.075.4536-0.11180.04070.0279-0.01670.0111-0.0406-0.54730.13970.02210.0861-0.02680.03680.10590.02070.135517.192-52.74990.095
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:4 )A2 - 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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