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- PDB-2zkn: X-ray structure of mutant galectin-1/lactose complex -

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Basic information

Entry
Database: PDB / ID: 2zkn
TitleX-ray structure of mutant galectin-1/lactose complex
ComponentsGalectin-1
KeywordsAPOPTOSIS / beta sandwich / Acetylation / Lectin
Function / homology
Function and homology information


galectin complex / lactose binding / plasma cell differentiation / galactoside binding / myoblast differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / positive regulation of inflammatory response ...galectin complex / lactose binding / plasma cell differentiation / galactoside binding / myoblast differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / positive regulation of inflammatory response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / collagen-containing extracellular matrix / positive regulation of viral entry into host cell / positive regulation of apoptotic process / endoplasmic reticulum lumen / apoptotic process / RNA binding / extracellular space / extracellular exosome / extracellular region / 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-lactose / Galectin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsAbe, A. / Yoshida, H. / Kamitori, S.
CitationJournal: Glycobiology / Year: 2008
Title: Functional and structural bases of a cysteine-less mutant as a long-lasting substitute for galectin-1
Authors: Nishi, N. / Abe, A. / Iwaki, J. / Yoshida, H. / Itoh, A. / Shoji, H. / Kamitori, S. / Hirabayashi, J. / Nakamura, T.
History
DepositionMar 26, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2008Provider: 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 / 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_assembly_gen / struct_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Nov 1, 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

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Assembly

Deposited unit
A: Galectin-1
B: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3483
Polymers29,0062
Non-polymers3421
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8452
Polymers14,5031
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Galectin-1


Theoretical massNumber of molelcules
Total (without water)14,5031
Polymers14,5031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.925, 87.431, 95.698
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 / Lectin galactoside-binding soluble 1 / Beta-galactoside-binding lectin L-14-I / Lactose-binding ...Lectin galactoside-binding soluble 1 / Beta-galactoside-binding lectin L-14-I / Lactose-binding lectin 1 / S-Lac lectin 1 / Galaptin / 14 kDa lectin / HPL / HBL / Putative MAPK-activating protein PM12


Mass: 14503.086 Da / Num. of mol.: 2 / Mutation: C2S, C16S, C42S, C60S, C88S, C130S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS1 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P09382
#2: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.66 Å3/Da / Density % sol: 53.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.0M ammonium sulfate, 20mM phosphate buffer, 5mM lactose, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 25, 2005 / Details: mirrors
RadiationMonochromator: A triangular silicon (111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→34.02 Å / Num. all: 26434 / Num. obs: 26434 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 13.7
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.184 / Num. unique all: 2236 / % possible all: 96.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W6O

1w6o


Resolution: 1.86→34.02 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 57920.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2625 9.9 %RANDOM
Rwork0.215 ---
obs0.215 26434 98.6 %-
all-26434 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.965 Å2 / ksol: 0.39075 e/Å3
Displacement parametersBiso mean: 19.3 Å2
Baniso -1Baniso -2Baniso -3
1-5.72 Å20 Å20 Å2
2---3.5 Å20 Å2
3----2.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 1.86→34.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2050 0 23 147 2220
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.8
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it2.222
X-RAY DIFFRACTIONc_scbond_it2.22
X-RAY DIFFRACTIONc_scangle_it3.282.5
LS refinement shellResolution: 1.86→1.93 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.261 298 11.8 %
Rwork0.214 2236 -
obs-2236 96.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1rotein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4carbohydrate.paramcarbohydrate.top

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