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- PDB-3ap7: Crystal structure of the galectin-8 N-terminal carbohydrate recog... -

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Basic information

Entry
Database: PDB / ID: 3ap7
TitleCrystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with lactose sialic acid
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 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 12, 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / 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 / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 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-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0923
Polymers17,4231
Non-polymers6692
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.360, 49.917, 70.289
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-8 / Gal-8 / Po66 carbohydrate-binding protein / Po66-CBP / Prostate carcinoma tumor antigen 1 / PCTA-1


Mass: 17423.123 Da / Num. of mol.: 1 / 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 N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 633.552 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.275mM protein, 10mM Hepes-NaOH, 2.75mM lactose sialic acid, 50mM sodium chloride, 0.5mM DTT, 80mM ammonium fluoride, 7.5% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 24, 2005
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→24.961 Å / Num. all: 25280 / Num. obs: 25280 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.8 % / Biso Wilson estimate: 14.014 Å2 / Rmerge(I) obs: 0.034 / Rsym value: 0.034
Reflection shellResolution: 1.53→1.57 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.192 / Mean I/σ(I) obs: 12.4 / Num. unique all: 1826 / Rsym value: 0.192 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AP5

3ap5


Resolution: 1.53→24.96 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.087 / SU ML: 0.041 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R Free: 0.073 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18828 1282 5.1 %RANDOM
Rwork0.16373 ---
all0.16493 23937 --
obs0.16493 23937 100 %-
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: 11.776 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2---0.13 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.53→24.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1204 0 44 222 1470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221300
X-RAY DIFFRACTIONr_bond_other_d0.0010.02893
X-RAY DIFFRACTIONr_angle_refined_deg1.2991.9811769
X-RAY DIFFRACTIONr_angle_other_deg0.7942.9982185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5935150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.02723.7162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.59615216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.095159
X-RAY DIFFRACTIONr_chiral_restr0.0830.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211395
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02262
X-RAY DIFFRACTIONr_mcbond_it0.7391.5756
X-RAY DIFFRACTIONr_mcbond_other0.1551.5304
X-RAY DIFFRACTIONr_mcangle_it1.32821241
X-RAY DIFFRACTIONr_scbond_it1.8123544
X-RAY DIFFRACTIONr_scangle_it2.94.5528
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 79 -
Rwork0.18 1735 -
obs-1814 100 %

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