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- PDB-8jjq: Structure of SenB in complex with UDP-GalNAc at 1.64 Angstroms re... -

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Basic information

Entry
Database: PDB / ID: 8jjq
TitleStructure of SenB in complex with UDP-GalNAc at 1.64 Angstroms resolution
ComponentsTIGR04348 family glycosyltransferase
KeywordsTRANSFERASE / UDP-GalNAc
Function / homologyPutative glycosyltransferase / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / TIGR04348 family glycosyltransferase
Function and homology information
Biological speciesVariovorax paradoxus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsFeng, L. / Wei, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2024
Title: Substrate binding and catalytic mechanism of the Se-glycosyltransferase SenB in the biosynthesis of selenoneine.
Authors: Huang, W. / Song, J. / Sun, T. / He, Y. / Li, X. / Deng, Z. / Long, F.
History
DepositionMay 31, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Aug 20, 2025Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: TIGR04348 family glycosyltransferase
A: TIGR04348 family glycosyltransferase
B: TIGR04348 family glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7986
Polymers105,9763
Non-polymers1,8223
Water19,7261095
1
C: TIGR04348 family glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9332
Polymers35,3251
Non-polymers6071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-5 kcal/mol
Surface area13140 Å2
MethodPISA
2
A: TIGR04348 family glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9332
Polymers35,3251
Non-polymers6071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-6 kcal/mol
Surface area12990 Å2
MethodPISA
3
B: TIGR04348 family glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9332
Polymers35,3251
Non-polymers6071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-5 kcal/mol
Surface area12950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.114, 56.377, 108.130
Angle α, β, γ (deg.)90.00, 91.01, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein TIGR04348 family glycosyltransferase


Mass: 35325.277 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Variovorax paradoxus (bacteria) / Gene: JF629_18585 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A952K6X5
#2: Chemical ChemComp-UD2 / URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / (2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate


Mass: 607.354 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H27N3O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1095 / Source method: isolated from a natural source / Formula: H2O
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: 3.21 Å3/Da / Density % sol: 61.63 %
Crystal growTemperature: 291.153 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 5000-MME, 0.1M Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.64→49.99 Å / Num. obs: 157933 / % possible obs: 98.8 % / Redundancy: 6.2 % / CC1/2: 0.997 / Net I/σ(I): 13.2
Reflection shellResolution: 1.64→1.67 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6787 / CC1/2: 0.655

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Processing

Software
NameVersionClassification
Blu-Ice5.8.0267data collection
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→49.99 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.197 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.017 / ESU R Free: 0.016 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19542 7648 4.8 %RANDOM
Rwork0.17595 ---
obs0.17691 150266 93.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.534 Å2
Baniso -1Baniso -2Baniso -3
1-2.29 Å20 Å25.41 Å2
2---3.81 Å2-0 Å2
3---1.52 Å2
Refinement stepCycle: 1 / Resolution: 1.64→49.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7206 0 117 1095 8418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0137471
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177161
X-RAY DIFFRACTIONr_angle_refined_deg1.9681.63710182
X-RAY DIFFRACTIONr_angle_other_deg1.5131.57616358
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0795955
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.76219.854411
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.225151141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7221584
X-RAY DIFFRACTIONr_chiral_restr0.10.2968
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.028588
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021777
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0131.823838
X-RAY DIFFRACTIONr_mcbond_other2.011.8193837
X-RAY DIFFRACTIONr_mcangle_it2.7642.7294787
X-RAY DIFFRACTIONr_mcangle_other2.7652.7294788
X-RAY DIFFRACTIONr_scbond_it2.7812.0673633
X-RAY DIFFRACTIONr_scbond_other2.782.0673634
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0383.0045396
X-RAY DIFFRACTIONr_long_range_B_refined5.70123.9888424
X-RAY DIFFRACTIONr_long_range_B_other5.36722.8678110
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.64→1.653 Å
RfactorNum. reflection% reflection
Rfree0.256 162 -
Rwork0.222 3006 -
obs--25.71 %

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