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- PDB-2zqn: Crystal structure of the earthworm R-type lectin C-half in comple... -

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Basic information

Entry
Database: PDB / ID: 2zqn
TitleCrystal structure of the earthworm R-type lectin C-half in complex with Lactose
Components29-kDa galactose-binding lectin
KeywordsSUGAR BINDING PROTEIN / EARTHWORM LUMBRICUS TERRESTRIS / HEMAGGLUTININ / R-TYPE LECTIN / BETA-TREFOIL FOLD / SUGAR COMPLEX / Lectin
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
beta-lactose / IMIDAZOLE / PHOSPHATE ION / 29-kDa galactose-binding lectin
Similarity search - Component
Biological speciesLumbricus terrestris (common earthworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSuzuki, R. / Kuno, A. / Hasegawa, T. / Hirabayashi, J. / Kasai, K. / Momma, M. / Fujimoto, Z.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Sugar-complex structures of the C-half domain of the galactose-binding lectin EW29 from the earthworm Lumbricus terrestris
Authors: Suzuki, R. / Kuno, A. / Hasegawa, T. / Hirabayashi, J. / Kasai, K. / Momma, M. / Fujimoto, Z.
#1: 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 Lumbricus terrestris
Authors: Suzuki, R. / Fujimoto, Z. / Kuno, A. / Hirabayashi, J. / Kasai, K. / Hasegawa, T.
#2: 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.
#3: 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
DepositionAug 13, 2008Deposition site: PDBJ / Processing site: PDBJ
SupersessionSep 2, 2008ID: 2D12
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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_struct_special_symmetry / 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.type_symbol / _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.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: 29-kDa galactose-binding lectin
B: 29-kDa galactose-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,19010
Polymers29,4932
Non-polymers1,6978
Water5,134285
1
A: 29-kDa galactose-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7597
Polymers14,7471
Non-polymers1,0136
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 29-kDa galactose-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4313
Polymers14,7471
Non-polymers6852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.166, 61.166, 175.597
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-437-

HOH

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Components

#1: Protein 29-kDa galactose-binding lectin


Mass: 14746.550 Da / Num. of mol.: 2 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lumbricus terrestris (common earthworm)
Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: O96048
#2: Polysaccharide
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.78 Å3/Da / Density % sol: 55.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: sodium chloride, dipotassium hydrogen phosphate, sodium dihydrogen phosphate, imidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 3, 2003
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 27297 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 22.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2660 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XYF

1xyf


Resolution: 1.9→42.29 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.764 / SU ML: 0.083 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22547 1366 5 %RANDOM
Rwork0.17645 ---
obs0.1788 25849 99.95 %-
all-27228 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.103 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2100 0 112 285 2497
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222264
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.9943078
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6025260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57626.19105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75715383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.125156
X-RAY DIFFRACTIONr_chiral_restr0.10.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021654
X-RAY DIFFRACTIONr_nbd_refined0.1890.21000
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21537
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2261
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.215
X-RAY DIFFRACTIONr_mcbond_it0.8861.51354
X-RAY DIFFRACTIONr_mcangle_it1.45322135
X-RAY DIFFRACTIONr_scbond_it2.22231039
X-RAY DIFFRACTIONr_scangle_it3.634.5943
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 111 -
Rwork0.208 1849 -
obs-2660 100 %

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