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- PDB-3w59: Crystal structure of Galectin-1 in the lactose-unbound state(P212121) -

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Basic information

Entry
Database: PDB / ID: 3w59
TitleCrystal structure of Galectin-1 in the lactose-unbound state(P212121)
ComponentsGalectin-1
KeywordsSUGAR BINDING PROTEIN / lactose unbound state / Galectin / lectin
Function / homology
Function and homology information


galectin complex / lactose binding / negative regulation of T-helper 17 cell lineage commitment / myoblast differentiation / plasma cell differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) ...galectin complex / lactose binding / negative regulation of T-helper 17 cell lineage commitment / myoblast differentiation / plasma cell differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of inflammatory response / : / regulation of apoptotic process / positive regulation of viral entry into host cell / positive regulation of canonical NF-kappaB signal transduction / positive regulation of apoptotic process / receptor ligand activity / endoplasmic reticulum lumen / apoptotic process / extracellular space / RNA binding / extracellular exosome / extracellular region / plasma membrane / cytoplasm / cytosol
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
BETA-MERCAPTOETHANOL / Galectin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSaburi, H. / Tanaka, T. / Kunishima, N.
CitationJournal: To be Published
Title: Crystal structure of Galectin-1 in the lactose-unbound state
Authors: Saburi, H. / Tanaka, T. / Kunishima, N.
History
DepositionJan 26, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)59,19713
Polymers58,3984
Non-polymers7999
Water6,287349
1
A: Galectin-1
B: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7148
Polymers29,1992
Non-polymers5156
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Galectin-1
D: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4835
Polymers29,1992
Non-polymers2843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.140, 111.557, 117.192
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Galectin-1 / Gal-1 / 14 kDa laminin-binding protein / HLBP14 / 14 kDa lectin / Beta-galactoside-binding lectin L- ...Gal-1 / 14 kDa laminin-binding protein / HLBP14 / 14 kDa lectin / Beta-galactoside-binding lectin L-14-I / Galaptin / HBL / HPL / Lactose-binding lectin 1 / Lectin galactoside-binding soluble 1 / Putative MAPK-activating protein PM12 / S-Lac lectin 1


Mass: 14599.477 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09382
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 3.25 Å3/Da / Density % sol: 62.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 2.0M ammonium sulfate, 1% 2-Mercaptoethanol, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.979 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 29, 2011
RadiationMonochromator: bending magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→47.19 Å / Num. all: 45407 / Num. obs: 45407 / % possible obs: 100 % / Biso Wilson estimate: 17.86 Å2
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 11.1 / % possible all: 100

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Processing

Software
NameVersionClassification
BSSdata collection
MOLREPphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GZW

1gzw


Resolution: 2.1→47.19 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2251 5 %RANDOM
Rwork0.212 ---
obs0.212 45339 99.6 %-
all-45407 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.9227 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 20.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-0 Å2
2---0.58 Å2-0 Å2
3---0.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.1→47.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4070 0 45 349 4464
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scbond_it2.262
X-RAY DIFFRACTIONc_scangle_it3.322.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.239 343 4.6 %
Rwork0.221 7066 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6bme_param.txtbme_top.txt
X-RAY DIFFRACTION7glycerol_param.txtglycerol_top.txt

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