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- PDB-7yro: Crystal structure of mango fucosyltransferase 13 -

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Basic information

Entry
Database: PDB / ID: 7yro
TitleCrystal structure of mango fucosyltransferase 13
ComponentsFucosyltransferase
KeywordsTRANSFERASE / fucosyltransferase / FUT13 / mango
Function / homology
Function and homology information


fucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / Golgi cisterna membrane / protein glycosylation
Similarity search - Function
Alpha-(1, 3)-fucosyltransferase/alpha-(1, 4)-fucosyltransferase, plant / Glycosyl transferase family 10 / GT10-like, C-terminal domain superfamily / Glycosyltransferase family 10 (fucosyltransferase) C-term
Similarity search - Domain/homology
ACETIC ACID / PHOSPHATE ION / PYROPHOSPHATE / Fucosyltransferase
Similarity search - Component
Biological speciesMangifera indica (mango)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsOkada, T. / Teramoto, T. / Ihara, H. / Ikeda, Y. / Kakuta, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20K06019 Japan
CitationJournal: Glycobiology / Year: 2024
Title: Crystal structure of mango alpha 1,3/ alpha 1,4-fucosyltransferase elucidates unique elements that regulate Lewis A-dominant oligosaccharide assembly.
Authors: Okada, T. / Teramoto, T. / Ihara, H. / Ikeda, Y. / Kakuta, Y.
History
DepositionAug 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fucosyltransferase
B: Fucosyltransferase
C: Fucosyltransferase
D: Fucosyltransferase
E: Fucosyltransferase
F: Fucosyltransferase
G: Fucosyltransferase
H: Fucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)374,09049
Polymers369,2898
Non-polymers4,80141
Water8,485471
1
A: Fucosyltransferase
B: Fucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,21310
Polymers92,3222
Non-polymers8918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-24 kcal/mol
Surface area26410 Å2
MethodPISA
2
C: Fucosyltransferase
D: Fucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,10217
Polymers92,3222
Non-polymers1,77915
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-28 kcal/mol
Surface area26590 Å2
MethodPISA
3
E: Fucosyltransferase
F: Fucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,79314
Polymers92,3222
Non-polymers1,47112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-19 kcal/mol
Surface area26560 Å2
MethodPISA
4
G: Fucosyltransferase
H: Fucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9838
Polymers92,3222
Non-polymers6606
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-25 kcal/mol
Surface area26530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.700, 163.610, 274.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 13 molecules ABCDEFGH

#1: Protein
Fucosyltransferase


Mass: 46161.164 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mangifera indica (mango) / Gene: FUT13 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: A0A292GKJ7, Transferases; Glycosyltransferases; Hexosyltransferases
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 507 molecules

#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: H4O7P2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.64 Å3/Da / Density % sol: 53.41 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Calcium acetate hydrate and 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.42→50 Å / Num. obs: 149646 / % possible obs: 100 % / Redundancy: 9.78 % / CC1/2: 0.995 / Net I/σ(I): 8.55
Reflection shellResolution: 2.42→2.56 Å / Mean I/σ(I) obs: 1.14 / Num. unique obs: 24409 / CC1/2: 0.544

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: predicted model

Resolution: 2.42→46.86 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2476 2000 1.34 %
Rwork0.2104 --
obs0.2109 149503 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.42→46.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21036 0 292 471 21799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00421944
X-RAY DIFFRACTIONf_angle_d0.69729834
X-RAY DIFFRACTIONf_dihedral_angle_d12.8277797
X-RAY DIFFRACTIONf_chiral_restr0.0543211
X-RAY DIFFRACTIONf_plane_restr0.0053794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.480.3271410.317110435X-RAY DIFFRACTION100
2.48-2.550.32971420.307110420X-RAY DIFFRACTION100
2.55-2.620.37671410.305210423X-RAY DIFFRACTION100
2.62-2.710.35791420.292310431X-RAY DIFFRACTION100
2.71-2.80.3311410.285210457X-RAY DIFFRACTION100
2.8-2.920.33011420.271910408X-RAY DIFFRACTION100
2.92-3.050.3181410.256510467X-RAY DIFFRACTION100
3.05-3.210.2991430.24710527X-RAY DIFFRACTION100
3.21-3.410.27871420.235310482X-RAY DIFFRACTION100
3.41-3.670.2161420.202810518X-RAY DIFFRACTION100
3.67-4.040.22811440.191810581X-RAY DIFFRACTION100
4.04-4.630.19991440.163710602X-RAY DIFFRACTION100
4.63-5.830.19611460.167110717X-RAY DIFFRACTION100
5.83-46.860.2081490.17711035X-RAY DIFFRACTION100

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