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- PDB-4y26: Complex of human Galectin-7 and Galbeta1-3(6OSO3)GlcNAc -

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Basic information

Entry
Database: PDB / ID: 4y26
TitleComplex of human Galectin-7 and Galbeta1-3(6OSO3)GlcNAc
ComponentsGalectin-7
KeywordsSUGAR BINDING PROTEIN / Complex / Galectin-7 / sulfated LacNAc / Galbeta1-3(6OSO3)GlcNAc
Function / homology
Function and homology information


Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / carbohydrate binding / apoptotic process / extracellular space / extracellular exosome / nucleus / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.611 Å
AuthorsLin, H.Y. / Hsieh, T.J. / Lin, C.H.
Funding support Taiwan, 4items
OrganizationGrant numberCountry
Academia SinicaAS-022316 Taiwan
Ministry of Science and Technology103-2113-M-001-023-MY3 Taiwan
Ministry of Science and Technology102-2113-M-001-001-MY3 Taiwan
Ministry of Science and Technology102-2923-M-001-001-MY3 Taiwan
CitationJournal: To Be Published
Title: Structural basis of human galectin-1 inhibition with Ki values in the micro- to nanomolar range
Authors: Lin, H.Y. / Hsieh, T.J. / Tu, Z. / Huang, B.S. / Chien, C.T. / Wu, S.C. / Hsu, S.T. / Lin, C.H.
History
DepositionFeb 9, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_oper_list / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 2.1Mar 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galectin-7
B: Galectin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0894
Polymers34,1342
Non-polymers9552
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.098, 55.404, 138.804
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Galectin-7 / Gal-7 / HKL-14 / PI7 / p53-induced gene 1 protein


Mass: 17067.236 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS7, PIG1, LGALS7B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P47929
#2: Polysaccharide beta-D-galactopyranose-(1-3)-methyl 2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranoside


Type: oligosaccharide / Mass: 477.439 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGalpb1-3DGlcpNAc[1Me,6S]b1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_1*OC_2*NCC/3=O_6*OSO/3=O/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-GlcpNAc6SO3]{[(3+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 1.7 Å3/Da / Density % sol: 27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES (pH 7.5), 0.2M Li2SO4, 0.1M NaOAc, 25% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.61→30 Å / Num. obs: 7526 / % possible obs: 99 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.118 / Χ2: 1.003 / Net I/av σ(I): 13.274 / Net I/σ(I): 7.3 / Num. measured all: 42427
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.61-2.75.50.4387310.995100
2.7-2.815.80.3647411.00599.9
2.81-2.945.90.2677411.00899.9
2.94-3.095.90.2137301.00999.5
3.09-3.295.90.1537581.00499.9
3.29-3.545.80.1157261.00698.8
3.54-3.95.80.0977490.99898.3
3.9-4.465.70.0787520.99298.3
4.46-5.615.30.0737641.00798.5
5.61-304.90.0738341.00197.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Blu-Icedata extraction
HKL-2000data scaling
PHASER2.5.3phasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.611→27.613 Å / FOM work R set: 0.8043 / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2576 344 4.59 %
Rwork0.1975 7145 -
obs0.2002 7489 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.58 Å2 / Biso mean: 28.43 Å2 / Biso min: 13.94 Å2
Refinement stepCycle: final / Resolution: 2.611→27.613 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2088 0 62 64 2214
Biso mean--30.85 27.11 -
Num. residues----266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032204
X-RAY DIFFRACTIONf_angle_d0.6712994
X-RAY DIFFRACTIONf_chiral_restr0.026328
X-RAY DIFFRACTIONf_plane_restr0.003398
X-RAY DIFFRACTIONf_dihedral_angle_d13.561844
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6107-3.28830.29021820.238835033685100
3.2883-27.61470.23831620.17743642380498
Refinement TLS params.Method: refined / Origin x: -19.4173 Å / Origin y: 99.3441 Å / Origin z: 154.3258 Å
111213212223313233
T0.1354 Å2-0.0088 Å2-0.0009 Å2-0.229 Å2-0.0148 Å2--0.1579 Å2
L0.6525 °2-0.6978 °20.0627 °2-3.0121 °2-0.686 °2--0.5488 °2
S-0.0311 Å °-0.0671 Å °-0.0202 Å °-0.0252 Å °0.0668 Å °0.0086 Å °0.0232 Å °0.003 Å °-0.023 Å °
Refinement TLS groupSelection details: all

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