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- PDB-5eo8: Crystal structure of AOL(868) -

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Basic information

Entry
Database: PDB / ID: 5eo8
TitleCrystal structure of AOL(868)
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-beta-L-fucopyranoside / Fucose-specific lectin
Similarity search - Component
Biological speciesAspergillus oryzae RIB40 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0227
Polymers34,5761
Non-polymers1,4476
Water6,287349
1
A: Predicted protein
hetero molecules

A: Predicted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,04514
Polymers69,1512
Non-polymers2,89412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area2410 Å2
ΔGint-8 kcal/mol
Surface area23530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.595, 58.595, 397.601
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-748-

HOH

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Components

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


Mass: 34575.633 Da / Num. of mol.: 1
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-TFU / methyl 1-seleno-beta-L-fucopyranoside / (2S,3S,4R,5S,6R)-2-methyl-6-methylselanyl-oxane-3,4,5-triol / methyl 6-deoxy-1-seleno-beta-L-galactopyranoside / methyl 1-seleno-beta-L-fucoside / methyl 1-seleno-L-fucoside / methyl 1-seleno-fucoside / Methyl group


Type: L-saccharide / Mass: 241.144 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C7H14O4Se
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.85 Å3/Da / Density % sol: 56.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 1.0 M mono-Ammonium dihydrogen Phosphate, 0.1 M tri-Sodium Citrate dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→47.39 Å / Num. obs: 55524 / % possible obs: 100 % / Redundancy: 48.2 % / CC1/2: 1 / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.028 / Net I/σ(I): 24.2 / Num. measured all: 2675664 / Scaling rejects: 1
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
1.6-1.6348.53.9831.613172227170.9060.57299.9
8.76-47.3933.20.04380.11611348510.00799.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
Aimless0.2.13data scaling
SHELXphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.6→45.196 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1826 2565 5.1 %
Rwork0.1636 95508 -
obs0.1645 50320 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.9 Å2 / Biso mean: 28.1022 Å2 / Biso min: 13.4 Å2
Refinement stepCycle: final / Resolution: 1.6→45.196 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2444 0 156 349 2949
Biso mean--36.03 38.34 -
Num. residues----311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042584
X-RAY DIFFRACTIONf_angle_d1.0213525
X-RAY DIFFRACTIONf_chiral_restr0.036393
X-RAY DIFFRACTIONf_plane_restr0.004439
X-RAY DIFFRACTIONf_dihedral_angle_d11.905924
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6-1.61820.39671580.343732083366
1.6182-1.63720.33581800.31932033383
1.6372-1.65720.34151660.313231193285
1.6572-1.67820.38111870.288332063393
1.6782-1.70030.31161860.284931223308
1.7003-1.72350.3231630.262532873450
1.7235-1.74820.23811760.252630913267
1.7482-1.77430.24061980.233132133411
1.7743-1.8020.25351800.214931273307
1.802-1.83150.28981710.222232293400
1.8315-1.86310.21731680.205930963264
1.8631-1.8970.23841570.189532303387
1.897-1.93350.20291510.170131673318
1.9335-1.9730.18862080.167331553363
1.973-2.01590.19151510.15732683419
2.0159-2.06270.18251820.148831283310
2.0627-2.11430.18341750.153131893364
2.1143-2.17150.13371790.144932123391
2.1715-2.23540.16521580.142431523310
2.2354-2.30750.14821420.143232213363
2.3075-2.390.15351840.140431453329
2.39-2.48570.16681600.144532203380
2.4857-2.59880.15421680.140531823350
2.5988-2.73580.19091550.139731953350
2.7358-2.90720.15741450.1532393384
2.9072-3.13160.15071750.15331653340
3.1316-3.44670.15071960.136832103406
3.4467-3.94510.16191970.143931393336
3.9451-4.96950.15621660.13431833349
4.9695-45.21390.17791490.172532073356
Refinement TLS params.Method: refined / Origin x: 33.5635 Å / Origin y: 16.7181 Å / Origin z: 14.8868 Å
111213212223313233
T0.1521 Å2-0.0063 Å2-0.0016 Å2-0.1679 Å2-0.002 Å2--0.1558 Å2
L0.6471 °2-0.084 °20.2329 °2-0.6389 °2-0.1703 °2--1.064 °2
S0.0247 Å °0.0956 Å °-0.0367 Å °-0.0827 Å °0.0023 Å °-0.0062 Å °0.1381 Å °-0.0399 Å °0.0004 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 311
2X-RAY DIFFRACTION1allB6 - 5
3X-RAY DIFFRACTION1allS1 - 349

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