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- PDB-4bmb: Crystal structure of the N terminal domain of human Galectin 8 -

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Basic information

Entry
Database: PDB / ID: 4bmb
TitleCrystal structure of the N terminal domain of human Galectin 8
ComponentsGALECTIN-8
KeywordsSUGAR BINDING PROTEIN / CARBOHYDRATE RECOGNITION
Function / homology
Function and homology information


lymphatic endothelial cell migration / xenophagy / cellular response to virus / integrin binding / cytoplasmic vesicle / carbohydrate binding / extracellular space / membrane / 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-8
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.351 Å
AuthorsBuzamet, E. / Ruiz, F.M. / Menendez, M. / Romero, A. / Gabius, H.J. / Solis, D.
CitationJournal: FEBS J. / Year: 2014
Title: Natural Single Amino Acid Polymorphism (F19Y) in Human Galectin-8: Detection of Structural Alterations and Increased Growth-Regulatory Activity on Tumor Cells.
Authors: Ruiz, F.M. / Scholz, B.A. / Buzamet, E. / Kopitz, J. / Andre, S. / Menendez, M. / Romero, A. / Solis, D. / Gabius, H.J.
History
DepositionMay 7, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_conn_angle / struct_conn / struct_conn_type / 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.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: 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 / pdbx_initial_refinement_model
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-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5155
Polymers16,9931
Non-polymers5234
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.516, 49.516, 160.476
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2098-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein GALECTIN-8 / GAL-8 / PO66 CARBOHYDRATE-BINDING PROTEIN / PO66-CBP / PROSTATE CARCINOMA TUMOR ANTIGEN 1 / PCTA-1


Mass: 16992.561 Da / Num. of mol.: 1 / Fragment: N TERMINAL DOMAIN, RESIDUES 4-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O00214
#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

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Non-polymers , 4 types, 255 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.74 Å3/Da / Density % sol: 55.2 % / Description: NONE
Crystal growDetails: 20% W/V PEG 4000, 100 MM HEPES SODIUM SALT (PH 7.2) AND 10 MM ZINC CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.00591
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00591 Å / Relative weight: 1
ReflectionResolution: 1.35→47.31 Å / Num. obs: 43869 / % possible obs: 98.1 % / Observed criterion σ(I): 1.5 / Redundancy: 7.9 % / Biso Wilson estimate: 15.69 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.1
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 7.9 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.5 / % possible all: 93.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YV8

2yv8


Resolution: 1.351→26.932 Å / SU ML: 0.14 / σ(F): 1.4 / Phase error: 17.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1773 4152 5.1 %
Rwork0.1586 --
obs0.1595 43818 97.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.5 Å2
Refinement stepCycle: LAST / Resolution: 1.351→26.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1198 0 31 252 1481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061272
X-RAY DIFFRACTIONf_angle_d1.1681721
X-RAY DIFFRACTIONf_dihedral_angle_d25.424506
X-RAY DIFFRACTIONf_chiral_restr0.076195
X-RAY DIFFRACTIONf_plane_restr0.005221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3511-1.39940.30883850.30067563X-RAY DIFFRACTION95
1.3994-1.45540.26283770.26077715X-RAY DIFFRACTION97
1.4554-1.52160.23934420.23057675X-RAY DIFFRACTION97
1.5216-1.60190.20874020.18557742X-RAY DIFFRACTION98
1.6019-1.70220.16534740.16027722X-RAY DIFFRACTION98
1.7022-1.83360.18233970.14927833X-RAY DIFFRACTION98
1.8336-2.01810.15433990.14277823X-RAY DIFFRACTION99
2.0181-2.310.16874030.14167874X-RAY DIFFRACTION99
2.31-2.90970.17364810.15427889X-RAY DIFFRACTION100
2.9097-26.93780.16273920.14447781X-RAY DIFFRACTION98
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)
12.26811.51931.33575.25982.34633.0254-0.0939-0.18850.15240.0285-0.04930.1313-0.1634-0.10320.12840.15340.0211-0.02960.18960.02770.178810.6616-14.476121.5068
21.5959-0.14470.54681.245-0.25351.5333-0.01070.068-0.0016-0.0761-0.0102-0.13090.06540.13530.00350.0633-0.00120.00320.09230.01270.09516.2765-12.27967.5774
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 4:18)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 19:153)

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