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- PDB-5eo7: Crystal structure of AOL -

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Basic information

Entry
Database: PDB / ID: 5eo7
TitleCrystal structure of AOL
ComponentsPredicted proteinProtein structure prediction
KeywordsSUGAR BINDING PROTEIN / seleno-fucoses / phaing / lectin / Aspergillus oryzae
Function / homology
Function and homology information


fucose binding / intracellular organelle / early endosome
Similarity search - Function
Fucose-specific lectin / Fucose-specific lectin / Fungal fucose-specific lectin / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
methyl 1-seleno-alpha-L-fucopyranoside / Fucose-specific lectin
Similarity search - Component
Biological speciesAspergillus oryzae RIB40 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsKato, R. / Kiso, M. / Ishida, H. / Ando, H. / Suzuki, T. / Shimabukuro, S. / Makyio, H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: Six independent fucose-binding sites in the crystal structure of Aspergillus oryzae lectin
Authors: Makyio, H. / Shimabukuro, J. / Suzuki, T. / Imamura, A. / Ishida, H. / Kiso, M. / Ando, H. / Kato, R.
History
DepositionNov 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 20, 2024Group: 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: Predicted protein
B: Predicted protein
C: Predicted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,33522
Polymers103,3333
Non-polymers4,00119
Water6,089338
1
A: Predicted protein
hetero molecules

A: Predicted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,87718
Polymers68,8892
Non-polymers2,98816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_756-x+2,y,-z+3/21
2
B: Predicted protein
C: Predicted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,39613
Polymers68,8892
Non-polymers2,50811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.161, 196.852, 110.605
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Predicted protein / Protein structure prediction / lectin


Mass: 34444.438 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae RIB40 (mold) / Strain: RIB 40 / Gene: AO090001000189 / Production host: Aspergillus oryzae (mold) / References: UniProt: Q2UNX8
#2: Sugar
ChemComp-SFU / methyl 1-seleno-alpha-L-fucopyranoside / METHYL 6-DEOXY-1-SELENO-ALPHA-L-GALACTOPYRANOSIDE / methyl 1-seleno-alpha-L-fucoside / methyl 1-seleno-L-fucoside / methyl 1-seleno-fucoside


Type: L-saccharide / Mass: 241.144 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C7H14O4Se
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 3.3 Å3/Da / Density % sol: 62.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2% (v/v) PEG-400, 2.0 M Ammonium sulfate, 0.1 M HEPES-Na

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 24, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→38.68 Å / Num. obs: 60854 / % possible obs: 100 % / Redundancy: 7.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.057 / Net I/σ(I): 13 / Num. measured all: 455430
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.3-2.367.50.733.33364344610.9460.285100
10.29-38.686.40.04638.948077560.9980.01998.3

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Phasing

PhasingMethod: MAD
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-97.403-138.153-4.026SE48.051.17
2-98.352-103.85232.297SE44.290.93
3-95.799-141.674-7.089SE44.830.9
4-99.092-97.31814.935SE49.420.68
5-79.879-129.024-8.178SE50.120.85
6-86.658-155.7663.25SE53.730.77
7-95.739-91.41447.631SE47.810.72
8-48.415-29.74-106.618SE53.490.54
9-38.386-21.372-11.153SE48.170.55
10-44.958-11.042-98.815SE52.040.46
11-27.637-3.304-101.269SE63.590.46
12-2.248-34.506-65.707SE62.260.47
13-51.072-45.563-12.1SE62.540.51
14-37.536-33.43-25.918SE46.530.28
15-12.745-20.288-57.227SE92.910.48

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
SHARPphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.3→38.68 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2414 3077 5.07 %
Rwork0.2193 57667 -
obs0.2205 60744 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.21 Å2 / Biso mean: 45.1206 Å2 / Biso min: 16.31 Å2
Refinement stepCycle: final / Resolution: 2.3→38.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7308 0 410 338 8056
Biso mean--44.9 37.3 -
Num. residues----930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047708
X-RAY DIFFRACTIONf_angle_d0.85610518
X-RAY DIFFRACTIONf_chiral_restr0.0331161
X-RAY DIFFRACTIONf_plane_restr0.0031314
X-RAY DIFFRACTIONf_dihedral_angle_d12.7072634
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3-2.3360.34571210.327625862707
2.336-2.37420.30971230.301225992722
2.3742-2.41520.33461540.303825862740
2.4152-2.45910.31851280.292926232751
2.4591-2.50640.36451460.285325642710
2.5064-2.55750.29431440.278525782722
2.5575-2.61310.29951460.272525882734
2.6131-2.67390.27721340.260926062740
2.6739-2.74080.29791380.251526112749
2.7408-2.81480.30051330.250526042737
2.8148-2.89760.2661330.258725892722
2.8976-2.99110.28921500.263126332783
2.9911-3.0980.22661320.244726002732
3.098-3.2220.26921250.235526352760
3.222-3.36850.25941340.221426132747
3.3685-3.5460.22931540.210626102764
3.546-3.7680.21531550.196726162771
3.768-4.05870.20311430.172826412784
4.0587-4.46660.17841630.156826292792
4.4666-5.11160.18441490.152126502799
5.1116-6.43530.19321240.179127222846
6.4353-38.68970.21471480.214827842932
Refinement TLS params.Method: refined / Origin x: 101.73 Å / Origin y: 48.272 Å / Origin z: 84.42 Å
111213212223313233
T0.4445 Å2-0.0825 Å20.0022 Å2-0.3231 Å2-0.0001 Å2--0.3108 Å2
L-0.0226 °20.0196 °20.0332 °2--0.0299 °2-0.0245 °2--0.1295 °2
S-0.044 Å °-0.0026 Å °0.0052 Å °0.0127 Å °0.0221 Å °-0.019 Å °-0.0484 Å °-0.0698 Å °-0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 311
2X-RAY DIFFRACTION1allB2 - 311
3X-RAY DIFFRACTION1allC2 - 311
4X-RAY DIFFRACTION1allD1 - 15
5X-RAY DIFFRACTION1allE2 - 5
6X-RAY DIFFRACTION1allS1 - 338

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