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- PDB-3m2m: Rat galectin-1 complex with lactose -

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Basic information

Entry
Database: PDB / ID: 3m2m
TitleRat galectin-1 complex with lactose
ComponentsGalectin-1
KeywordsCarbohydrate-binding protein / galectin-1 / lectin / beta sandwich / Extracellular matrix / Secreted
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 / response to isolation stress / plasma cell differentiation / negative regulation of cell-substrate adhesion / myoblast differentiation / cellular response to organic cyclic compound ...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 / 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 / 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
beta-lactose / Galectin-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsLobsanov, Y.D. / Rini, J.M. / Leffler, H.
CitationJournal: Biochemistry / Year: 2010
Title: Monovalent interactions of galectin-1.
Authors: Salomonsson, E. / Larumbe, A. / Tejler, J. / Tullberg, E. / Rydberg, H. / Sundin, A. / Khabut, A. / Frejd, T. / Lobsanov, Y.D. / Rini, J.M. / Nilsson, U.J. / Leffler, H.
History
DepositionMar 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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 / struct_conn / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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
E: Galectin-1
F: Galectin-1
G: Galectin-1
H: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,90013
Polymers118,1898
Non-polymers1,7115
Water0
1
A: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1162
Polymers14,7741
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Galectin-1


Theoretical massNumber of molelcules
Total (without water)14,7741
Polymers14,7741
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1162
Polymers14,7741
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1162
Polymers14,7741
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1162
Polymers14,7741
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Galectin-1


Theoretical massNumber of molelcules
Total (without water)14,7741
Polymers14,7741
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Galectin-1


Theoretical massNumber of molelcules
Total (without water)14,7741
Polymers14,7741
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1162
Polymers14,7741
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
A: Galectin-1
B: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8903
Polymers29,5472
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
C: Galectin-1
D: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2324
Polymers29,5472
Non-polymers6852
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
E: Galectin-1
F: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8903
Polymers29,5472
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
G: Galectin-1
H: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8903
Polymers29,5472
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.100, 58.600, 121.600
Angle α, β, γ (deg.)101.100, 91.600, 110.900
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Galectin-1 / / Gal-1 / Lectin galactoside-binding soluble 1 / Beta-galactoside-binding lectin L-14-I / Lactose- ...Gal-1 / Lectin galactoside-binding soluble 1 / Beta-galactoside-binding lectin L-14-I / Lactose-binding lectin 1 / S-Lac lectin 1 / Galaptin / 14 kDa lectin / RL 14.5


Mass: 14773.625 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Lgals1 / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / References: UniProt: P11762
#2: Polysaccharide
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE

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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: 2.2 Å3/Da / Density % sol: 44.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 30mM NaOAc, PEG 4K 15-17%, 4mM 2-mercaptoethanol, 100mM lactose, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 Å
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 2, 1993 / Details: mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.95→500 Å / Num. all: 15682 / Num. obs: 15682 / % possible obs: 73.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.95→3.08 Å / % possible all: 42.3

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
MERLOTphasing
GLRFphasing
INTREFphasing
X-PLORphasing
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→36 Å / Occupancy max: 1 / Occupancy min: 0.7 / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The crystals show a pseudo-centred packing arrangement and diffract x-rays anisotropically and although data to 2.95 A was included in the refinement, weak and/or missing reflections lead to ...Details: The crystals show a pseudo-centred packing arrangement and diffract x-rays anisotropically and although data to 2.95 A was included in the refinement, weak and/or missing reflections lead to an effective resolution of 3.4 A (with a 2 sigma cutoff) as calculated by DATAMAN ("Software and Resources for Macromolecular Crystallography and Structural Biology" program package from the Uppsala Software Factory). NCS was used in the refinement of this structure as follows. Group 1: chains A, C, D, E and H. Group 2: chains B, F and G with the exception of residues 49, 50, 69-74 and 81 in each chain. Group 1: weight = 300, target sigma = 2, rmsd for NCS B restraints = 1.049. Group 2: weight = 300, target sigma = 2, rmsd for NCS B restraints = 0.967. The positional rmsd's between monomers are: A-C = 0.0274, A-D = 0.0986, A-E = 0.0317. A-H = 0.1001, B-F = 0.0293, and B-G = 0.0257.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1076 5.1 %Random
Rwork0.206 ---
all0.233 15682 --
obs0.233 15682 73.7 %-
Solvent computationBsol: 12.947 Å2
Displacement parametersBiso max: 68.12 Å2 / Biso mean: 28.005 Å2 / Biso min: 8.87 Å2
Baniso -1Baniso -2Baniso -3
1-5.904 Å23.235 Å2-7.271 Å2
2---4.588 Å2-1.972 Å2
3----1.316 Å2
Refinement stepCycle: LAST / Resolution: 2.95→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7961 0 115 0 8076
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1361.5
X-RAY DIFFRACTIONc_scbond_it1.4642
X-RAY DIFFRACTIONc_mcangle_it2.0372
X-RAY DIFFRACTIONc_scangle_it2.432.5
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.33
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep+cso.param
X-RAY DIFFRACTION2carbohydrate.param

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