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- PDB-1iuc: Fucose-specific lectin from Aleuria aurantia with three ligands -

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Basic information

Entry
Database: PDB / ID: 1iuc
TitleFucose-specific lectin from Aleuria aurantia with three ligands
ComponentsFucose-specific lectin
KeywordsSUGAR BINDING PROTEIN / Lectin / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


reproductive fruiting body development / fucose binding / defense response to fungus / carbohydrate binding / protein homodimerization activity / identical protein binding
Similarity search - Function
Fucose-specific lectin / Fucose-specific lectin / Fungal fucose-specific lectin / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
alpha-L-fucopyranose / beta-L-fucopyranose / Fucose-specific lectin
Similarity search - Component
Biological speciesAleuria aurantia (orange peel mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.24 Å
AuthorsFujihashi, M. / Peapus, D.H. / Kamiya, N. / Nagata, Y. / Miki, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: Biochemistry / Year: 2003
Title: Crystal Structure of Fucose-Specific Lectin from Aleuria aurantia Binding Ligands at Three of Its Five Sugar Recognition Sites
Authors: Fujihashi, M. / Peapus, D.H. / Kamiya, N. / Nagata, Y. / Miki, K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: X-ray crystallographic characterization and phasing of a fucose-specific lectin from Aleuria aurantia
Authors: Fujihashi, M. / Peapus, D.H. / Nakajima, E. / Yamada, T. / Saito, J.I. / Kita, A. / Higuchi, Y. / Sugawara, Y. / Ando, A. / Kamiya, N. / Nagata, Y. / Miki, K.
History
DepositionMar 1, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fucose-specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0155
Polymers33,4261
Non-polymers5894
Water3,045169
1
A: Fucose-specific lectin
hetero molecules

A: Fucose-specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,02910
Polymers66,8522
Non-polymers1,1778
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Unit cell
Length a, b, c (Å)84.032, 84.032, 250.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Fucose-specific lectin


Mass: 33425.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aleuria aurantia (orange peel mushroom)
Plasmid: pKA-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P18891
#2: Sugar ChemComp-FUL / beta-L-fucopyranose / beta-L-fucose / 6-deoxy-beta-L-galactopyranose / L-fucose / fucose / 6-DEOXY-BETA-L-GALACTOSE / Fucose


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-fucopyranoseCOMMON NAMEGMML 1.0
b-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose / Fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 169 / 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: 3.81 Å3/Da / Density % sol: 67.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: potassium phosphate, sodium chloride, potassium chloride, ammonium sulfate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 297 K / Method: vapor diffusion, sitting drop
Details: Fujihashi, M., (2003) Acta Crystallogr.,Sect.D, 59, 378.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15 mg/mlprotein1drop
28 mMsodium phosphate1reservoir
31.5 mMpotassium phosphate1reservoir
4137 mM1reservoirNaCl
52.7 mM1reservoirKClpH7.2
620 mMbeta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jun 16, 1998
RadiationMonochromator: Silicon (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.24→50 Å / Num. all: 46319 / Num. obs: 46319 / % possible obs: 91.2 % / Observed criterion σ(I): 1 / Redundancy: 8.1 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 31.3
Reflection shellResolution: 2.24→2.29 Å / Rmerge(I) obs: 0.301 / % possible all: 81.2
Reflection
*PLUS
Lowest resolution: 100 Å
Reflection shell
*PLUS
% possible obs: 81.2 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.24→39.83 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2387171.8 / 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
Rfree0.196 2292 5 %RANDOM
Rwork0.164 ---
all-46265 --
obs-46265 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.7864 Å2 / ksol: 0.323438 e/Å3
Displacement parametersBiso mean: 30.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20.66 Å20 Å2
2---1.45 Å20 Å2
3---2.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.24→39.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 38 169 2576
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.921.5
X-RAY DIFFRACTIONc_mcangle_it3.842
X-RAY DIFFRACTIONc_scbond_it4.522
X-RAY DIFFRACTIONc_scangle_it5.672.5
LS refinement shellResolution: 2.24→2.38 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.236 362 5 %
Rwork0.204 6895 -
obs--91.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION5CIS_PEPTIDE.PARAM
Refinement
*PLUS
Lowest resolution: 40 Å / Num. reflection obs: 46425 / Rfactor Rwork: 0.165
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77
LS refinement shell
*PLUS
Rfactor Rfree: 0.23 / Rfactor Rwork: 0.207

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