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- PDB-2dry: Crystal structure of the earthworm lectin C-terminal domain mutant -

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Basic information

Entry
Database: PDB / ID: 2dry
TitleCrystal structure of the earthworm lectin C-terminal domain mutant
Components29-kDa galactose-binding lectin
KeywordsSUGAR BINDING PROTEIN / EARTHWORM LUMBRICUS TERRESTRIS / SIALIC ACID / GALACTOSE / IN VITRO EVOLUTION / BETA-TREFOIL FOLD
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
TRIETHYLENE GLYCOL / 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 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 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)29,5498
Polymers28,8642
Non-polymers6856
Water4,540252
1
A: 29-kDa galactose-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9676
Polymers14,4321
Non-polymers5345
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 29-kDa galactose-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5822
Polymers14,4321
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.151, 89.562, 41.670
Angle α, β, γ (deg.)90.00, 116.39, 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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.32 Å3/Da / Density % sol: 47.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30% PEGMME2000, 0.2M Ammonium Sulfate, 0.1M Sodium Acetate trihydrate , pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Feb 6, 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: 41322 / Num. obs: 21395 / % possible obs: 87.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 761.8 / Biso Wilson estimate: 19 Å2
Reflection shellResolution: 1.8→1.86 Å / % possible all: 82.3

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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→22.64 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 522944.62 / 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
Rfree0.263 1042 4.9 %RANDOM
Rwork0.234 ---
obs0.234 21367 86.7 %-
all-24577 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.5549 Å2 / ksol: 0.289893 e/Å3
Displacement parametersBiso mean: 25.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å21.31 Å2
2---0.21 Å20 Å2
3---0.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.8→22.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2040 0 40 252 2332
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.336 163 5 %
Rwork0.277 3099 -
obs-1989 80 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cis_peptide4F61.paramion.top
X-RAY DIFFRACTION3carbo_rep.paramwater.top
X-RAY DIFFRACTION4water_rep.paramcarbohydrate.top
X-RAY DIFFRACTION5ion.paramdna-rna.top

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