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

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Basic information

Entry
Database: PDB / ID: 3apb
TitleCrystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with iodide
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
IODIDE ION / Galectin-8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsMatsuzaka, T. / Ideo, H. / Yamashita, K. / Nonaka, T.
CitationJournal: To be Published
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 14, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galectin-8
B: Galectin-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,52631
Polymers34,8462
Non-polymers3,68029
Water2,918162
1
A: Galectin-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,07314
Polymers17,4231
Non-polymers1,65013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Galectin-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,45417
Polymers17,4231
Non-polymers2,03016
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.591, 75.869, 77.901
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.: 2 / 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: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.78 Å3/Da / Density % sol: 55.77 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.55mM protein, 10mM Hepes-NaOH, 50mM sodium chloride, 0.5mM DTT, 125mM ammonium fluoride, 8% 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: 1.3 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 3, 2005
RadiationMonochromator: Fixed exit Si 111 double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 1.947→38.954 Å / Num. all: 28969 / Num. obs: 28969 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.94→2.01 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.95→38.95 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.255 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.148 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24198 1408 4.9 %RANDOM
Rwork0.20151 ---
obs0.20342 27561 99.51 %-
all-27561 --
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: 23.384 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2---0.8 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.95→38.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2424 0 29 162 2615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222482
X-RAY DIFFRACTIONr_bond_other_d0.0010.021714
X-RAY DIFFRACTIONr_angle_refined_deg1.3181.9533364
X-RAY DIFFRACTIONr_angle_other_deg0.8134176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4985302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67323.793116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44215424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.471516
X-RAY DIFFRACTIONr_chiral_restr0.0830.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212744
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02510
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_it0.6891.51514
X-RAY DIFFRACTIONr_mcbond_other0.1561.5612
X-RAY DIFFRACTIONr_mcangle_it1.29322474
X-RAY DIFFRACTIONr_scbond_it1.9623968
X-RAY DIFFRACTIONr_scangle_it3.2774.5890
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.947→1.998 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 97 -
Rwork0.214 1883 -
obs-1980 93.79 %

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