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- PDB-4ga9: Crystal Structure of Rat Galectin-1 in Complex with Lactose -

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Basic information

Entry
Database: PDB / ID: 4ga9
TitleCrystal Structure of Rat Galectin-1 in Complex with Lactose
ComponentsGalectin-1
KeywordsCarbohydrate-binding protein / jellyroll like/beta barrel
Function / homology
Function and homology information


positive regulation of erythrocyte aggregation / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / lactose binding / galectin complex / galactoside binding / response to isolation stress / plasma cell differentiation / negative regulation of cell-substrate adhesion / myoblast differentiation ...positive regulation of erythrocyte aggregation / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / lactose binding / galectin complex / galactoside binding / response to isolation stress / plasma cell differentiation / negative regulation of cell-substrate adhesion / myoblast differentiation / cellular response to organic cyclic compound / response to axon injury / laminin binding / T cell costimulation / cellular response to glucose stimulus / cell-cell adhesion / positive regulation of inflammatory response / negative regulation of neuron projection development / carbohydrate binding / collagen-containing extracellular matrix / positive regulation of viral entry into host cell / response to xenobiotic stimulus / positive regulation of apoptotic process / apoptotic process / cell surface / extracellular space / identical protein binding / cytoplasm
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
alpha-lactose / Galectin-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å
AuthorsSegev, O. / Hirsch, J.A.
CitationJournal: to be published
Title: Gal-1 structure analysis
Authors: Segev, O. / Hirsch, J.A.
History
DepositionJul 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1404
Polymers29,4552
Non-polymers6852
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint4 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.388, 106.440, 107.978
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-329-

HOH

21B-348-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 4 / Auth seq-ID: 2 - 135 / Label seq-ID: 1 - 134

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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 / RL 14.5 / S-Lac lectin 1


Mass: 14727.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Lgals1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11762
#2: Polysaccharide beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / alpha-lactose


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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.59 Å3/Da / Density % sol: 52.59 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: Bis-Tris Propane, lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorDetector: CCD / Date: Aug 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.86→61.78 Å / Num. all: 27931 / Num. obs: 27931 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.86→1.929 Å / % possible all: 98.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.092 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2699 1264 5.1 %RANDOM
Rwork0.2155 ---
all0.2183 27931 --
obs0.2183 24817 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 87.56 Å2 / Biso mean: 39.281 Å2 / Biso min: 20.15 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20 Å20 Å2
2--1.12 Å20 Å2
3----2.38 Å2
Refinement stepCycle: LAST / Resolution: 1.88→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2062 0 46 167 2275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222155
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.9752922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2345266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.07725.577104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35815344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.546158
X-RAY DIFFRACTIONr_chiral_restr0.0720.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021636
X-RAY DIFFRACTIONr_nbd_refined0.1960.2827
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21442
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2161
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.218
X-RAY DIFFRACTIONr_mcbond_it2.71831365
X-RAY DIFFRACTIONr_mcangle_it3.81952134
X-RAY DIFFRACTIONr_scbond_it5.4727867
X-RAY DIFFRACTIONr_scangle_it7.69610788
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1031 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.280.5
MEDIUM THERMAL0.422
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 98 -
Rwork0.282 1726 -
all-1824 -
obs--99.89 %
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)
11.0335-0.0446-1.42871.2423-0.05637.4184-0.13190.1516-0.12550.0467-0.3887-0.13380.4534-0.35040.5205-0.20140.04240.036-0.1881-0.0377-0.1275-18.865713.4984-14.003
21.18040.0589-0.08820.9105-1.41847.33-0.38130.0263-0.12250.1351-0.1299-0.1239-0.33220.45570.5113-0.19630.0384-0.0364-0.19210.0399-0.1253-13.495518.853614.013
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 135
2X-RAY DIFFRACTION2B2 - 135

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