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- PDB-1iub: Fucose-specific lectin from Aleuria aurantia (Hg-derivative form) -

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Basic information

Entry
Database: PDB / ID: 1iub
TitleFucose-specific lectin from Aleuria aurantia (Hg-derivative form)
ComponentsFucose-specific lectin
KeywordsSUGAR BINDING PROTEIN / Hg / MAD / 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
beta-L-fucopyranose / : / Fucose-specific lectin
Similarity search - Component
Biological speciesAleuria aurantia (orange peel mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.31 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)34,3228
Polymers33,4261
Non-polymers8967
Water2,054114
1
A: Fucose-specific lectin
hetero molecules

A: Fucose-specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,64516
Polymers66,8522
Non-polymers1,79314
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)83.909, 83.909, 254.131
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein / Sugars , 2 types, 3 molecules A

#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


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

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Non-polymers , 4 types, 119 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 3.86 Å3/Da / Density % sol: 68.15 %
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
61 mM1reservoirHgCl2

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.00901, 1.00394, 0.918326
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jul 1, 1997
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.009011
21.003941
30.9183261
ReflectionResolution: 2.31→40 Å / Num. all: 43457 / Num. obs: 43457 / % possible obs: 95.4 % / Observed criterion σ(I): 1 / Redundancy: 11.2 % / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 27.2
Reflection shellResolution: 2.31→2.36 Å / Rmerge(I) obs: 0.29 / % possible all: 93
Reflection
*PLUS
Lowest resolution: 200 Å
Reflection shell
*PLUS
% possible obs: 93 % / Rmerge(I) obs: 0.29

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.31→35.97 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2231137.46 / 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
Rfree0.183 2162 5 %RANDOM
Rwork0.156 ---
all-43422 --
obs-43422 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.462 Å2 / ksol: 0.324721 e/Å3
Displacement parametersBiso mean: 37.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.22 Å2-1.07 Å20 Å2
2---2.22 Å20 Å2
3---4.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.31→35.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 31 114 2514
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it3.011.5
X-RAY DIFFRACTIONc_mcangle_it4.122
X-RAY DIFFRACTIONc_scbond_it4.42
X-RAY DIFFRACTIONc_scangle_it5.462.5
LS refinement shellResolution: 2.31→2.45 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.24 360 5.2 %
Rwork0.205 6586 -
obs--95.2 %
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 DIFFRACTION4FUC.paramFUC.top
X-RAY DIFFRACTION5cis_peptide.param
Refinement
*PLUS
Lowest resolution: 40 Å / Num. reflection obs: 43442 / Rfactor Rwork: 0.161
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9
LS refinement shell
*PLUS
Rfactor Rfree: 0.241 / Rfactor Rwork: 0.212

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