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- PDB-3ap4: Crystal structure of the galectin-8 N-terminal carbohydrate recog... -

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Basic information

Entry
Database: PDB / ID: 3ap4
TitleCrystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with lactose
ComponentsGalectin-8
KeywordsSUGAR BINDING PROTEIN / Beta-Sandwich / Galectin / Carbohydrate/Sugar Binding
Function / homology
Function and homology information


lymphatic endothelial cell migration / xenophagy / plasma cell differentiation / T cell costimulation / cellular response to virus / integrin binding / carbohydrate binding / cytoplasmic vesicle / extracellular space / membrane ...lymphatic endothelial cell migration / xenophagy / plasma cell differentiation / T cell costimulation / cellular response to virus / integrin binding / carbohydrate binding / cytoplasmic vesicle / 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
alpha-lactose / Galectin-8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsMatsuzaka, T. / Ideo, H. / Yamashita, K. / Nonaka, T.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Galectin-8-N-domain recognition mechanism for sialylated and sulfated glycans
Authors: Ideo, H. / Matsuzaka, T. / Nonaka, T. / Seko, A. / Yamashita, K.
History
DepositionOct 11, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 15, 2014Group: Database references
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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
Revision 2.1Mar 13, 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-8
B: Galectin-8
C: Galectin-8
D: Galectin-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0628
Polymers69,6924
Non-polymers1,3694
Water5,531307
1
A: Galectin-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7652
Polymers17,4231
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Galectin-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7652
Polymers17,4231
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Galectin-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7652
Polymers17,4231
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Galectin-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7652
Polymers17,4231
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.528, 64.888, 71.584
Angle α, β, γ (deg.)98.41, 105.49, 108.66
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Galectin-8 / Gal-8 / Po66 carbohydrate-binding protein / Po66-CBP / Prostate carcinoma tumor antigen 1 / PCTA-1


Mass: 17423.123 Da / Num. of mol.: 4 / Fragment: N-terminal carbohydrate recognition domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS8 / Plasmid: pGEX-6P-2 / Production host: Escherichia coli (E. coli) / References: UniProt: O00214
#2: Polysaccharide
beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / alpha-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS RESIDUE IS CAUSED BY NATURAL VARIANT.

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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: 2.44 Å3/Da / Density % sol: 49.68 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.275mM protein, 10mM Hepes-NaOH, 2.75mM lactose, 50mM sodium chloride, 0.5mM DTT, 50mM ammonium fluoride, 12% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.92 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 3, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.33→59.462 Å / Num. all: 26924 / Num. obs: 26924 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 23.253 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046
Reflection shellResolution: 2.33→2.39 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 10.7 / Num. unique all: 1581 / Rsym value: 0.06 / % possible all: 76.3

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→51.33 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.876 / SU B: 6.698 / SU ML: 0.165 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.45 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25138 1313 4.9 %RANDOM
Rwork0.19077 ---
obs0.19364 25610 95.48 %-
all-25610 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.209 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0.59 Å2-0.09 Å2
2---0.73 Å2-0.26 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.33→51.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4683 0 92 307 5082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224895
X-RAY DIFFRACTIONr_bond_other_d0.0010.023384
X-RAY DIFFRACTIONr_angle_refined_deg1.2051.9726641
X-RAY DIFFRACTIONr_angle_other_deg0.73838248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4655582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.49923.6225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88215818
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6271532
X-RAY DIFFRACTIONr_chiral_restr0.0720.2758
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215294
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02998
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.451.52915
X-RAY DIFFRACTIONr_mcbond_other0.0731.51180
X-RAY DIFFRACTIONr_mcangle_it0.84624766
X-RAY DIFFRACTIONr_scbond_it1.16931980
X-RAY DIFFRACTIONr_scangle_it1.9224.51875
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.33→2.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 88 -
Rwork0.192 1491 -
obs-1579 76.35 %

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