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- PDB-2ds0: Crystal structure of the earthworm lectin C-terminal domain mutan... -

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Basic information

Entry
Database: PDB / ID: 2ds0
TitleCrystal structure of the earthworm lectin C-terminal domain mutant in complex with 6'-sialyllactose
Components29-kDa galactose-binding lectin
KeywordsSUGAR BINDING PROTEIN / EARTHWORM LUMBRICUS TERRESTRIS / SIALIC ACID / GALACTOSE / IN VITRO EVOLUTION / BETA-TREFOIL FOLD / SUGAR COMPLEX
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
6'-sialyl-lactose / 29-kDa galactose-binding lectin
Similarity search - Component
Biological speciesLumbricus terrestris (common earthworm)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSuzuki, R. / Fujimoto, Z.
Citation
Journal: J.Biochem. / Year: 2007
Title: Tailoring a novel sialic acid-binding lectin from a ricin-B chain-like galactose-binding protein by natural evolution-mimicry
Authors: Yabe, R. / Suzuki, R. / Kuno, A. / Fujimoto, Z. / Jigami, Y. / Hirabayashi, J.
#1: Journal: To be Published / Year: 2006
Title: Sugar complex structures of the galactose-binding lectin EW29 C-half domain from the earthworm Lumbricus terrestris
Authors: Suzuki, R. / Kuno, A. / Hasegawa, T. / Hirabayashi, J. / Kasai, K. / Momma, M. / Fujimoto, Z.
#2: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004
Title: Crystallization and preliminary X-ray crystallographic studies of the C-terminal domain of galactose-binding lectin EW29 from the earthworm Lubmricus terrestris
Authors: Suzuki, R. / Fujimoto, Z. / Kuno, A. / Hirabayashi, J. / Kasai, K. / Hasegawa, T.
#3: Journal: To be Published / Year: 2006
Title: In vitro selection of carbohydrate-binding protein by using advanced ribosome display
Authors: Yabe, R. / Kuno, A. / Sawata, Y.S. / Hirabayashi, J. / Jigamai, Y. / Taira, K. / Hasegawa, T.
#4: Journal: J.Biol.Chem. / Year: 1998
Title: Novel galactose-binding proteins in Annelida. Characterization of 29-kDa tandem repeat-type lectins from the earthworm Lumbricus terrestris
Authors: Hirabayashi, J. / Dutta, S.K. / Kasai, K.
History
DepositionJun 16, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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 / pdbx_unobs_or_zero_occ_atoms / 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 / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 10, 2021Group: Advisory / Database references / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Oct 25, 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

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Assembly

Deposited unit
A: 29-kDa galactose-binding lectin
B: 29-kDa galactose-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6129
Polymers28,8642
Non-polymers1,7477
Water3,801211
1
A: 29-kDa galactose-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4506
Polymers14,4321
Non-polymers1,0185
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 29-kDa galactose-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1623
Polymers14,4321
Non-polymers7302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.435, 87.684, 41.384
Angle α, β, γ (deg.)90.00, 117.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 29-kDa galactose-binding lectin


Mass: 14432.154 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN / Mutation: E148G,I227N,D230G,I231V,E237G,G239S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lumbricus terrestris (common earthworm)
Plasmid: pET27 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: O96048
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / 6'-sialyl-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 633.552 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 6'-sialyl-lactose
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpb1-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_b6-c2WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 20% PEG8000, 0.2M sodium chloride, 0.1M phosphate-citrate, 15mg/ml 6'-sialyllactose, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Feb 27, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 44954 / Num. obs: 22875 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 14.3 Å2
Reflection shellResolution: 1.8→1.86 Å / % possible all: 93.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2D12

2d12
PDB Unreleased entry


Resolution: 1.8→22.88 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 964768.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1109 4.9 %RANDOM
Rwork0.209 ---
obs0.209 22852 95.7 %-
all-23791 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.2003 Å2 / ksol: 0.327187 e/Å3
Displacement parametersBiso mean: 17.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20.54 Å2
2---0.08 Å20 Å2
3---0.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.8→22.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2040 0 111 211 2362
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0.71
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.268 171 4.8 %
Rwork0.226 3415 -
obs-2202 90.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cis_peptide4F61SL.paramion.top
X-RAY DIFFRACTION3carbo_rep.paramwater.top
X-RAY DIFFRACTION4water_rep.paramcarbohydrate.top
X-RAY DIFFRACTION5ion.paramdna-rna.top

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