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- PDB-3vv1: Crystal Structure of Caenorhabditis elegans galectin LEC-6 -

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Basic information

Entry
Database: PDB / ID: 3vv1
TitleCrystal Structure of Caenorhabditis elegans galectin LEC-6
ComponentsProtein LEC-6
KeywordsSUGAR BINDING PROTEIN / Galectin / galactose-1 / 4-fucose binding
Function / homology
Function and homology information


Neutrophil degranulation / galactoside binding / carbohydrate binding / 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 speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMakyio, H. / Takeuchi, T. / Tamura, M. / Nishiyama, K. / Takahashi, H. / Natsugari, H. / Arata, Y. / Kasai, K. / Yamada, Y. / Wakatsuki, S. / Kato, R.
CitationJournal: Glycobiology / Year: 2013
Title: Structural basis of preferential binding of fucose-containing saccharide by the Caenorhabditis elegans galectin LEC-6
Authors: Makyio, H. / Takeuchi, T. / Tamura, M. / Nishiyama, K. / Takahashi, H. / Natsugari, H. / Arata, Y. / Kasai, K. / Yamada, Y. / Wakatsuki, S. / Kato, R.
History
DepositionJul 10, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 20, 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: Protein LEC-6
B: Protein LEC-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7007
Polymers34,9752
Non-polymers7265
Water6,684371
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint0 kcal/mol
Surface area12230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.323, 69.323, 120.131
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11B-203-

MG

21B-204-

MG

31A-488-

HOH

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Components

#1: Protein Protein LEC-6 / Galectin LEC-6


Mass: 17487.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: lec-6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9N384
#2: Polysaccharide beta-D-galactopyranose-(1-4)-alpha-L-fucopyranose


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4LFucpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1221m-1a_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-L-Fucp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 2.6 Å3/Da / Density % sol: 52.76 % / Mosaicity: 0.117 °
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5
Details: 25%(w/v) PEG3350, 100mM HEPES, 200mM MgCl2, pH 7.5, VAPOR DIFFUSION, temperature 289.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2010
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 52195 / Num. obs: 51811 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.096 / Χ2: 1.278 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.555.60.65150840.751198.4
1.55-1.625.70.48651730.81198.6
1.62-1.695.70.36951560.851198.8
1.69-1.785.70.26751580.956199.1
1.78-1.895.70.18251551.154199.2
1.89-2.045.70.13751751.589199.3
2.04-2.245.60.10652091.685199.6
2.24-2.565.60.09652041.64199.7
2.56-3.235.60.07752151.761199.8
3.23-505.40.06852821.586199.5

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 2.383 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1793 2640 5.1 %RANDOM
Rwork0.147 ---
obs0.1486 51775 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.85 Å2 / Biso mean: 18.1864 Å2 / Biso min: 7.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20.33 Å2-0 Å2
2--0.65 Å2-0 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2202 0 47 371 2620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022310
X-RAY DIFFRACTIONr_angle_refined_deg1.9181.923147
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9825279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72823.548124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.43715324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8721516
X-RAY DIFFRACTIONr_chiral_restr0.1520.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211816
X-RAY DIFFRACTIONr_rigid_bond_restr5.44932310
X-RAY DIFFRACTIONr_sphericity_free23.5735104
X-RAY DIFFRACTIONr_sphericity_bonded9.04452516
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 176 -
Rwork0.195 3548 -
all-3724 -
obs--98.36 %
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)
10.6011-0.3846-0.26361.68260.40583.01360.0278-0.01750.00040.015-0.0097-0.09020.02840.1225-0.01820.0083-0.0060.00890.0122-0.01040.026317.148149.204410.1872
20.7425-0.00720.07311.2924-0.37262.25940.0065-0.0247-0.02120.0763-0.0198-0.0824-0.03880.12290.01330.04220.0069-0.02990.02840.00810.031313.55825.559736.6324
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 146
2X-RAY DIFFRACTION1A201 - 203
3X-RAY DIFFRACTION2B7 - 146
4X-RAY DIFFRACTION2B201 - 204

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