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- PDB-8yrl: Crystal structure of Aspergillus fumigatus Galactofuranosylransfe... -

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Basic information

Entry
Database: PDB / ID: 8yrl
TitleCrystal structure of Aspergillus fumigatus Galactofuranosylransferase (AfGfsA) in complex with UDP and galactofuranose
ComponentsGlycosyltransferase family 31 protein
KeywordsTRANSFERASE / Galactofuranosylransferase galactofuranose
Function / homologyProtein of unknown function DUF604 / Protein of unknown function, DUF604 / membrane / beta-D-galactofuranose / : / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase family 31 protein
Function and homology information
Biological speciesAspergillus fumigatus CEA10 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.37 Å
AuthorsOkuno, A. / Oka, T. / Chihara, Y. / Hirata, R. / Kadooka, C. / Teramoto, T. / Hira, D. / Kakuta, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Pnas Nexus / Year: 2024
Title: Substrate binding and catalytic mechanism of UDP-alpha-D-galactofuranose: beta-galactofuranoside beta-(1→5)-galactofuranosyltransferase GfsA.
Authors: Oka, T. / Okuno, A. / Hira, D. / Teramoto, T. / Chihara, Y. / Hirata, R. / Kadooka, C. / Kakuta, Y.
History
DepositionMar 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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.title / _citation.year / _citation_author.name
Revision 1.2Nov 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyltransferase family 31 protein
B: Glycosyltransferase family 31 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,95819
Polymers112,6662
Non-polymers2,29217
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-60 kcal/mol
Surface area36300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.142, 188.606, 71.933
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Glycosyltransferase family 31 protein


Mass: 56333.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus CEA10 (mold) / Strain: CEA10 / Gene: AFUB_096220 / Production host: Escherichia coli (E. coli) / References: UniProt: B0YDN6
#5: Sugar ChemComp-GZL / beta-D-galactofuranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalfbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactofuranoseCOMMON NAMEGMML 1.0
b-D-GalfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 333 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris (pH 5.5), 28% (w/v) polyethylene glycol 3350

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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: Jun 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.37→47.34 Å / Num. obs: 47069 / % possible obs: 99.5 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rsym value: 0.087 / Net I/σ(I): 14.4
Reflection shellResolution: 2.37→2.46 Å / Mean I/σ(I) obs: 2.55 / Num. unique obs: 4542 / CC1/2: 0.927 / Rsym value: 0.666

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
XSCALEdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.37→47.34 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 31.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2682 2410 5.12 %
Rwork0.2059 --
obs0.209 47026 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.37→47.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7402 0 142 318 7862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.492
X-RAY DIFFRACTIONf_dihedral_angle_d15.5562877
X-RAY DIFFRACTIONf_chiral_restr0.0541139
X-RAY DIFFRACTIONf_plane_restr0.0031368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.420.37271170.31512495X-RAY DIFFRACTION96
2.42-2.470.35071420.28192602X-RAY DIFFRACTION100
2.47-2.530.31541600.26952563X-RAY DIFFRACTION100
2.53-2.590.37261420.26612584X-RAY DIFFRACTION100
2.59-2.660.3141610.24892595X-RAY DIFFRACTION100
2.66-2.740.33611550.25622574X-RAY DIFFRACTION100
2.74-2.830.2651520.23982600X-RAY DIFFRACTION100
2.83-2.930.36471380.24342593X-RAY DIFFRACTION100
2.93-3.050.34041350.24922635X-RAY DIFFRACTION100
3.05-3.190.3111290.23172606X-RAY DIFFRACTION100
3.19-3.360.29621500.22542643X-RAY DIFFRACTION100
3.36-3.570.27761330.22472614X-RAY DIFFRACTION100
3.57-3.840.26661550.19792628X-RAY DIFFRACTION100
3.84-4.230.221390.17052656X-RAY DIFFRACTION100
4.23-4.840.19541090.15392700X-RAY DIFFRACTION100
4.84-6.10.22221410.17232717X-RAY DIFFRACTION100
6.1-47.340.22411520.1772811X-RAY DIFFRACTION99

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