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- PDB-3wud: X-ray crystal structure of Xenopus laevis galectin-Ib -

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Basic information

Entry
Database: PDB / ID: 3wud
TitleX-ray crystal structure of Xenopus laevis galectin-Ib
ComponentsGalectin
KeywordsSUGAR BINDING PROTEIN / Beta-Sandwich / Lectin / Carbohydrate/Sugar Binding
Function / homology
Function and homology information


carbohydrate binding
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
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsNonaka, Y. / Yoshida, H. / Kamitori, S. / Nakamura, T.
CitationJournal: Glycobiology / Year: 2015
Title: Crystal structure of a Xenopus laevis skin proto-type galectin, close to but distinct from galectin-1.
Authors: Nonaka, Y. / Ogawa, T. / Yoshida, H. / Shoji, H. / Nishi, N. / Kamitori, S. / Nakamura, T.
History
DepositionApr 23, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / 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_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 24, 2022Group: Database references / Structure summary / Category: chem_comp / citation / database_2
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8063
Polymers15,3671
Non-polymers4382
Water88349
1
A: Galectin
hetero molecules

A: Galectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6116
Polymers30,7352
Non-polymers8774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1130 Å2
ΔGint-8 kcal/mol
Surface area11840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.210, 35.320, 58.510
Angle α, β, γ (deg.)90.00, 111.82, 90.00
Int Tables number5
Space group name H-MC121
DetailsAUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN

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Components

#1: Protein Galectin


Mass: 15367.341 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: lgals1, xgalectin-Ib / Plasmid: pGEX4T-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q98UD4
#2: Polysaccharide beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / alpha-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: 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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.1 Å3/Da / Density % sol: 41.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 34% PEG 3350, 0.1M MES, 0.2M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Nov 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.68→18.92 Å / Num. all: 13973 / Num. obs: 13973 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.04 % / Biso Wilson estimate: 31.8 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 14.3
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 4.04 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1334 / % possible all: 91.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.7.0032refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WUC

3wuc


Resolution: 1.68→18.92 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.63 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25329 710 5.1 %RANDOM
Rwork0.19716 ---
obs0.2 13263 94.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.589 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å2-1.47 Å2
2--0.63 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.68→18.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1055 0 28 49 1132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191116
X-RAY DIFFRACTIONr_bond_other_d0.0010.021024
X-RAY DIFFRACTIONr_angle_refined_deg2.1521.9691509
X-RAY DIFFRACTIONr_angle_other_deg0.9733.0022367
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5595135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93425.53656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.34215194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.734153
X-RAY DIFFRACTIONr_chiral_restr0.160.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021256
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02261
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_it2.0761.984531
X-RAY DIFFRACTIONr_mcbond_other2.0761.982530
X-RAY DIFFRACTIONr_mcangle_it2.8472.969663
X-RAY DIFFRACTIONr_mcangle_other2.8452.971664
X-RAY DIFFRACTIONr_scbond_it3.4442.357585
X-RAY DIFFRACTIONr_scbond_other3.4412.339581
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.133.357839
X-RAY DIFFRACTIONr_long_range_B_refined6.63716.11133
X-RAY DIFFRACTIONr_long_range_B_other6.58116.0221128
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 55 -
Rwork0.341 927 -
obs--91.09 %

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