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- PDB-4xbq: Crystal Structure of Human Galectin-7 in Complex with Type 1 N-ac... -

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Basic information

Entry
Database: PDB / ID: 4xbq
TitleCrystal Structure of Human Galectin-7 in Complex with Type 1 N-acetyllactosamine
ComponentsGalectin-7
KeywordsSUGAR BINDING PROTEIN / Complex / Human Galectin-7 / Type 1 LacNAc
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 / Resolution: 2.234 Å
AuthorsHsieh, T.J. / Lin, H.Y. / 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: Plos One / Year: 2015
Title: Structural Basis Underlying the Binding Preference of Human Galectins-1, -3 and -7 for Gal beta 1-3/4GlcNAc.
Authors: Hsieh, T.J. / Lin, H.Y. / Tu, Z. / Huang, B.S. / Wu, S.C. / Lin, C.H.
History
DepositionDec 17, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation_wavelength / entity / entity_src_gen / 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 / _chem_comp.name / _chem_comp.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _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 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)35,0414
Polymers34,2742
Non-polymers7672
Water1,13563
1
A: Galectin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5212
Polymers17,1371
Non-polymers3831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galectin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5212
Polymers17,1371
Non-polymers3831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.085, 55.411, 136.497
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-7 / Gal-7 / HKL-14 / PI7 / p53-induced gene 1 protein


Mass: 17137.221 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS7, PIG1, LGALS7B / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P47929
#2: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGalpb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 1.66 Å3/Da / Density % sol: 25.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes pH 7.5, 0.2M Lithium Sulfate, 0.1M Sodium Acetate, 25% (w/v) PEG 4000, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2336→30 Å / Num. obs: 11562 / % possible obs: 98.7 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/av σ(I): 14.59 / Net I/σ(I): 14.59
Reflection shellResolution: 2.2336→2.3134 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 6.21 / % possible all: 96.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data processing
SCALEPACKdata scaling
PHASERphasing
PHENIXmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BKZ

1bkz


Resolution: 2.234→22.86 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2245 545 4.72 %
Rwork0.1956 --
obs0.197 11554 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.234→22.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2088 0 52 63 2203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032194
X-RAY DIFFRACTIONf_angle_d0.8112978
X-RAY DIFFRACTIONf_dihedral_angle_d14.127838
X-RAY DIFFRACTIONf_chiral_restr0.032326
X-RAY DIFFRACTIONf_plane_restr0.005398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2336-2.45820.31631300.21022674X-RAY DIFFRACTION98
2.4582-2.81330.24461430.23312732X-RAY DIFFRACTION100
2.8133-3.54240.22891330.20542748X-RAY DIFFRACTION99
3.5424-22.86120.19681390.17342855X-RAY DIFFRACTION98

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