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- PDB-4lbq: Crystal structure of mouse galectin-1 -

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Basic information

Entry
Database: PDB / ID: 4lbq
TitleCrystal structure of mouse galectin-1
Components(Galectin-1) x 3
KeywordsSUGAR BINDING PROTEIN / beta-sandwich / beta-galactosides binding / regulator of immunity / Secreted / extracellular space / extracellular matrix
Function / homology
Function and homology information


positive regulation of erythrocyte aggregation / lactose binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / response to xenobiotic stimulus => GO:0009410 / response to isolation stress / galactose binding / plasma cell differentiation / negative regulation of cell-substrate adhesion / myoblast differentiation ...positive regulation of erythrocyte aggregation / lactose binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / response to xenobiotic stimulus => GO:0009410 / response to isolation stress / galactose binding / plasma cell differentiation / negative regulation of cell-substrate adhesion / myoblast differentiation / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / cellular response to organic cyclic compound / response to axon injury / laminin binding / T cell costimulation / cellular response to glucose stimulus / negative regulation of neuron projection development / carbohydrate binding / collagen-containing extracellular matrix / positive regulation of viral entry into host cell / apoptotic process / cell surface / extracellular space / extracellular region / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRustiguel, J.K. / Trabuco, A.C. / Del Cistia Andrade, C. / Stowell, S.R. / Cummings, R.D. / Dias-Baruffi, M. / Nonato, M.C.
CitationJournal: To be Published
Title: Crystal structure of mouse galectin-1
Authors: Rustiguel, J.K. / Trabuco, A.C. / Del Cistia Andrade, C. / Stowell, S.R. / Cummings, R.D. / Dias-Baruffi, M. / Nonato, M.C.
History
DepositionJun 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 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-1
B: Galectin-1
C: Galectin-1
D: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9488
Polymers59,5794
Non-polymers3684
Water4,360242
1
A: Galectin-1
D: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9984
Polymers29,8142
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-5 kcal/mol
Surface area11790 Å2
MethodPISA
2
B: Galectin-1
C: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9504
Polymers29,7662
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-8 kcal/mol
Surface area11910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.040, 38.200, 130.180
Angle α, β, γ (deg.)90.00, 112.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Galectin-1 / / Gal-1 / 14 kDa lectin / Beta-galactoside-binding lectin L-14-I / Galaptin / Lactose-binding lectin ...Gal-1 / 14 kDa lectin / Beta-galactoside-binding lectin L-14-I / Galaptin / Lactose-binding lectin 1 / Lectin galactoside-binding soluble 1 / S-Lac lectin 1


Mass: 14898.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gbp, Lgals1 / Plasmid: pET29a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P16045
#2: Protein Galectin-1 / / Gal-1 / 14 kDa lectin / Beta-galactoside-binding lectin L-14-I / Galaptin / Lactose-binding lectin ...Gal-1 / 14 kDa lectin / Beta-galactoside-binding lectin L-14-I / Galaptin / Lactose-binding lectin 1 / Lectin galactoside-binding soluble 1 / S-Lac lectin 1


Mass: 14882.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gbp, Lgals1 / Plasmid: pET29a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P16045
#3: Protein Galectin-1 / / Gal-1 / 14 kDa lectin / Beta-galactoside-binding lectin L-14-I / Galaptin / Lactose-binding lectin ...Gal-1 / 14 kDa lectin / Beta-galactoside-binding lectin L-14-I / Galaptin / Lactose-binding lectin 1 / Lectin galactoside-binding soluble 1 / S-Lac lectin 1


Mass: 14914.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gbp, Lgals1 / Plasmid: pET29a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P16045
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 20% PEG 3350, 0.2 M ammonium fluoride, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 26, 2010
Details: Collimating mirror, Si(111) double-crystal monochromator and toroidal bendable mirror
RadiationMonochromator: Si(111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 2.4→35.752 Å / Num. obs: 19975 / % possible obs: 99.88 % / Observed criterion σ(F): 1.35 / Observed criterion σ(I): 1.7 / Redundancy: 3.8 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.444 / Rsym value: 0.444 / Net I/σ(I): 4.5
Reflection shellResolution: 2.4→2.5267 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2.5 / Num. unique all: 39013 / Rsym value: 0.444 / % possible all: 99.88

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M2M

3m2m


Resolution: 2.4→35.75 Å / SU ML: 0.3 / Isotropic thermal model: overall / σ(F): 1.35 / σ(I): 1.7 / Phase error: 24.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 1018 5.1 %Random
Rwork0.1858 ---
obs0.1884 19975 99.88 %-
all-39013 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→35.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3936 0 24 242 4202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044106
X-RAY DIFFRACTIONf_angle_d0.8625581
X-RAY DIFFRACTIONf_dihedral_angle_d13.341453
X-RAY DIFFRACTIONf_chiral_restr0.033617
X-RAY DIFFRACTIONf_plane_restr0.004751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.52670.30971560.25652658X-RAY DIFFRACTION100
2.5267-2.68490.29341440.23722663X-RAY DIFFRACTION100
2.6849-2.89210.29911600.22562681X-RAY DIFFRACTION100
2.8921-3.1830.30061370.21442694X-RAY DIFFRACTION100
3.183-3.64320.22941330.17632709X-RAY DIFFRACTION100
3.6432-4.58850.20231430.14472726X-RAY DIFFRACTION100
4.5885-35.75620.19111450.17232826X-RAY DIFFRACTION100
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)
13.2377-2.09623.85657.9998-3.61026.004-0.1920.3310.06670.041-0.0592-0.6322-0.2686-0.08020.48020.3340.17610.06380.38050.0560.4134-33.07548.3936134.5274
24.76870.5012-1.6743.57071.02152.9976-0.3824-0.1346-1.03650.09560.0652-0.06350.5606-0.12240.22080.32010.11840.03910.32020.08590.5538-44.0659-3.4628137.3731
33.98170.0882-0.51563.21911.93332.3785-0.0599-0.2784-0.2918-0.0082-0.07010.36550.0761-0.29880.11560.27670.0809-0.0160.33030.05720.3433-49.24426.5694140.6805
43.57013.4481-0.67787.91960.27021.9216-0.04460.03650.0925-0.20220.04620.58590.12170.0447-0.07540.34270.059-0.00310.38340.04610.3219-45.53966.7774128.2272
56.5622-2.01670.32894.96620.61612.32250.06330.34660.2819-0.3303-0.31630.1471-0.4558-0.14720.24140.40550.0932-0.01330.34790.07510.2916-43.664916.0656133.0737
63.47712.36750.0672.27131.04082.84070.23180.2456-0.74780.5434-0.2270.62220.2104-0.4215-0.140.2524-0.01770.00940.40960.02840.4207-39.24642.5502141.9259
78.18885.1573-6.23133.4739-4.80398.72160.35540.4510.4857-0.49830.10290.7298-0.3268-0.663-0.2630.42290.1434-0.02010.35670.02110.3766-36.0524-1.4466132.0554
86.00643.8427-5.08537.6417-3.89464.2954-0.1817-0.1295-0.4575-0.51550.1701-0.69980.52280.19580.30920.36470.0366-0.02510.4358-0.02030.3878-24.959115.4242166.3663
94.6610.40371.09421.8727-0.00970.9219-0.08530.2140.5107-0.06970.118-0.1595-0.1365-0.06540.00480.26720.08170.01890.41010.04040.4056-30.791424.8972162.3193
104.56461.43821.57334.90712.21033.1867-0.0239-0.1390.89-0.3581-0.18150.4204-0.5552-0.46720.20440.3810.11680.03750.47230.05630.5798-38.562428.1095161.8794
112.52411.895-0.513.6951-0.54271.71330.25860.14110.60930.77840.1270.4903-0.278-0.2997-0.37130.37420.08060.0430.4167-0.05930.3948-34.921923.8494173.1056
127.85053.0736-0.55813.48060.45471.98630.1348-0.08360.61160.0934-0.01080.422-0.1217-0.1109-0.12990.25060.10880.01410.37820.0310.3434-28.099419.6564165.5168
137.57975.7984-3.72414.4924-3.12047.9377-0.0622-0.0005-0.1609-0.4792-0.0902-1.11530.0221-0.01640.31670.27340.07220.08280.37680.10.5867-13.80219.83159.538
144.4621-1.7112.42163.8695-2.38782.4350.1879-0.08610.39671.196-0.40610.1186-0.576-0.0943-0.08460.45550.09010.12680.3798-0.03410.4723-11.20517.589171.734
153.108-0.9668-0.20172.6059-2.25486.40720.07810.0816-0.3603-0.13-0.26820.04340.10650.57820.22870.20890.0271-0.02660.3756-0.03460.3681-7.6468.637163.097
165.0254-0.5582-0.02280.86962.01653.7-0.0257-0.043-0.4260.12750.1348-0.31120.69790.98790.01650.3860.1233-0.04150.4090.07430.4326-0.4025.959166.615
174.8792-1.0786-0.54092.44081.68874.60160.29740.18580.959-0.15450.1304-0.3632-0.30150.8952-0.38270.2853-0.00570.03220.3773-0.00030.4846-1.51719.287162.282
186.3253-4.5151-1.46685.46431.74778.18450.083-0.3347-0.27940.2175-0.04290.10080.0213-0.2844-0.09260.19340.0059-0.03330.32460.01380.3167-14.07115.242167.455
194.7861-3.20080.61843.4632-2.00263.566-0.2967-0.2365-0.54550.63160.2882-0.2064-0.194-0.17930.02950.24530.1007-0.02160.40520.03270.5339-27.429-4.571139.392
205.66830.3183-2.44936.6688-3.9443.21140.04530.83930.3924-0.8961-0.4642-0.26030.54070.60490.04280.47450.2037-0.00810.69990.13670.5231-23.792-1.011125.916
216.2709-2.34651.75031.88350.11321.17780.09120.16030.83080.0348-0.1151-0.2891-0.36480.2881-0.21590.30910.10460.03510.39190.04960.4199-15.4480.765136.257
224.3019-1.06151.50783.1743-0.41024.99790.01020.3654-0.1186-0.3480.1949-0.1061-0.26830.65510.03030.33110.07310.03630.5218-0.0080.4571-9.718-2.902133.989
233.2943-0.0682-0.4743.4041-0.6024.20650.2624-0.4106-0.58090.08070.1790.79880.12830.1443-0.17190.34190.10370.02110.4444-0.03630.5077-19.945-10.962133.902
247.9197-2.20324.0595.9619-3.38943.01910.24741.0507-0.7757-0.5408-0.1622-0.41030.98770.71050.15390.34790.13990.03470.5589-0.11460.5868-14.369-12.613130.492
257.7471-3.94512.73032.3625-1.43993.6652-0.2441-0.3178-0.01230.27240.2440.0683-0.1949-0.1733-0.02110.32480.0997-0.00690.45710.05490.4934-22.584-2.825137.81
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 3:16)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 17:32)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 33:84)
4X-RAY DIFFRACTION4CHAIN A AND (RESID 85:105)
5X-RAY DIFFRACTION5CHAIN A AND (RESID 106:119)
6X-RAY DIFFRACTION6CHAIN A AND (RESID 120:126)
7X-RAY DIFFRACTION7CHAIN A AND (RESID 127:135)
8X-RAY DIFFRACTION8CHAIN B AND (RESID 3:16)
9X-RAY DIFFRACTION9CHAIN B AND (RESID 17:49)
10X-RAY DIFFRACTION10CHAIN B AND (RESID 50:84)
11X-RAY DIFFRACTION11CHAIN B AND (RESID 85:110)
12X-RAY DIFFRACTION12CHAIN B AND (RESID 111:135)
13X-RAY DIFFRACTION13CHAIN C AND (RESID 3:16)
14X-RAY DIFFRACTION14CHAIN C AND (RESID 17:24)
15X-RAY DIFFRACTION15CHAIN C AND (RESID 25:49)
16X-RAY DIFFRACTION16CHAIN C AND (RESID 50:84)
17X-RAY DIFFRACTION17CHAIN C AND (RESID 85:119)
18X-RAY DIFFRACTION18CHAIN C AND (RESID 120:135)
19X-RAY DIFFRACTION19CHAIN D AND (RESID 3:18)
20X-RAY DIFFRACTION20CHAIN D AND (RESID 19:24)
21X-RAY DIFFRACTION21CHAIN D AND (RESID 25:49)
22X-RAY DIFFRACTION22CHAIN D AND (RESID 50:84)
23X-RAY DIFFRACTION23CHAIN D AND (RESID 85:100)
24X-RAY DIFFRACTION24CHAIN D AND (RESID 101:110)
25X-RAY DIFFRACTION25CHAIN D AND (RESID 111:135)

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