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- PDB-5h47: Crystal structure of AOL complexed with 2-MeSe-Fuc -

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Basic information

Entry
Database: PDB / ID: 5h47
TitleCrystal structure of AOL complexed with 2-MeSe-Fuc
ComponentsUncharacterized protein
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
Chem-FSW / Fucose-specific lectin
Similarity search - Component
Biological speciesAspergillus oryzae RIB40 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsKato, R. / Nishikawa, Y. / Makyio, H.
CitationJournal: Bioorg. Med. Chem. / Year: 2017
Title: Synthesis of seleno-fucose compounds and their application to the X-ray structural determination of carbohydrate-lectin complexes using single/multi-wavelength anomalous dispersion phasing
Authors: Shimabukuro, J. / Makyio, H. / Suzuki, T. / Nishikawa, Y. / Kawasaki, M. / Imamura, A. / Ishida, H. / Ando, H. / Kato, R. / Kiso, M.
History
DepositionOct 31, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Aug 30, 2017Group: Data collection / Category: diffrn_detector / diffrn_source
Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / 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 1.4Mar 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.mon_nstd_flag / _chem_comp.pdbx_synonyms ..._chem_comp.mon_nstd_flag / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
G: Uncharacterized protein
H: Uncharacterized protein
I: Uncharacterized protein
J: Uncharacterized protein
K: Uncharacterized protein
L: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)433,28084
Polymers414,90812
Non-polymers18,37272
Water29,5631641
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1077
Polymers34,5761
Non-polymers1,5316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1077
Polymers34,5761
Non-polymers1,5316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1077
Polymers34,5761
Non-polymers1,5316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1077
Polymers34,5761
Non-polymers1,5316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1077
Polymers34,5761
Non-polymers1,5316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1077
Polymers34,5761
Non-polymers1,5316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1077
Polymers34,5761
Non-polymers1,5316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1077
Polymers34,5761
Non-polymers1,5316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1077
Polymers34,5761
Non-polymers1,5316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1077
Polymers34,5761
Non-polymers1,5316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1077
Polymers34,5761
Non-polymers1,5316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1077
Polymers34,5761
Non-polymers1,5316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.972, 214.316, 126.531
Angle α, β, γ (deg.)90.00, 108.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Uncharacterized protein / fucose-specific lectin


Mass: 34575.633 Da / Num. of mol.: 12
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) / Strain (production host): O-1018 / References: UniProt: Q2UNX8
#2: Sugar...
ChemComp-FSW / methyl 6-deoxy-2-Se-methyl-2-seleno-alpha-L-galactopyranoside / (2S,3S,4R,5S,6R)-6-methoxy-2-methyl-5-methylselanyl-oxane-3,4-diol / methyl 6-deoxy-2-Se-methyl-2-seleno-alpha-L-galactoside / methyl 6-deoxy-2-Se-methyl-2-seleno-L-galactoside / methyl 6-deoxy-2-Se-methyl-2-seleno-galactoside


Type: L-saccharide / Mass: 255.170 Da / Num. of mol.: 72 / Source method: obtained synthetically / Formula: C8H16O4Se
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1641 / 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: 3.29 Å3/Da / Density % sol: 62.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Tryptone, HEPES, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→49.05 Å / Num. obs: 270453 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 28.3 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.213 / Net I/σ(I): 8.9
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.837 / Mean I/σ(I) obs: 1 / CC1/2: 0.63 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→39.99 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.915 / SU B: 0.002 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25838 11932 5 %RANDOM
Rwork0.21588 ---
obs0.21801 224805 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.674 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0.01 Å2
2---0.03 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.3→39.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29232 0 936 1641 31809
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 909 -
Rwork0.351 16505 -
obs--100 %

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