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

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Basic information

Entry
Database: PDB / ID: 2zqo
TitleCrystal structure of the earthworm R-type lectin C-half in complex with GalNAc
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
: / IMIDAZOLE / 2-acetamido-2-deoxy-beta-D-galactopyranose / PHOSPHATE ION / 29-kDa galactose-binding lectin
Similarity search - Component
Biological speciesLumbricus terrestris (common earthworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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: 2AO3
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 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)30,58611
Polymers29,2352
Non-polymers1,3519
Water5,675315
1
A: 29-kDa galactose-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3366
Polymers14,6171
Non-polymers7195
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)15,2505
Polymers14,6171
Non-polymers6324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.210, 34.747, 61.586
Angle α, β, γ (deg.)90.00, 104.20, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-515-

HOH

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Components

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Protein / Sugars , 2 types, 6 molecules AB

#1: Protein 29-kDa galactose-binding lectin


Mass: 14617.369 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: Sugar
ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE / N-Acetylgalactosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 320 molecules

#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.19 Å3/Da / Density % sol: 43.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: sodium chloride, dipotassium hydrogen phosphate, sodium dihydrogen phosphate, imidazole, cadmium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 5, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 23141 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 36.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 8.6 / Num. unique all: 2213 / % possible all: 94

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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: 1.8→48.62 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.9 / SU B: 2.766 / SU ML: 0.09 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25981 1190 5.1 %RANDOM
Rwork0.19212 ---
obs0.19542 21951 97.08 %-
all-23837 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.126 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2077 0 81 315 2473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222204
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.9712990
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3265258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13226105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.56915373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.329157
X-RAY DIFFRACTIONr_chiral_restr0.0950.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021650
X-RAY DIFFRACTIONr_nbd_refined0.1930.2999
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21496
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2275
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2520.231
X-RAY DIFFRACTIONr_mcbond_it0.8821.51339
X-RAY DIFFRACTIONr_mcangle_it1.43722109
X-RAY DIFFRACTIONr_scbond_it2.1993988
X-RAY DIFFRACTIONr_scangle_it3.3064.5881
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 85 -
Rwork0.192 1495 -
obs-2213 91.81 %

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