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- PDB-8rz3: Structures of Se- glycosyltransferase SenB from Variovorax paradoxus -

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Basic information

Entry
Database: PDB / ID: 8rz3
TitleStructures of Se- glycosyltransferase SenB from Variovorax paradoxus
ComponentsTIGR04348 family glycosyltransferase
KeywordsSTRUCTURAL PROTEIN / C-Se bond formation / glycosyltransferase
Function / homologyPutative glycosyltransferase / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / TIGR04348 family glycosyltransferase
Function and homology information
Biological speciesVariovorax paradoxus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMa, Y.Y. / Gao, Y. / Xu, S.H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32394010 China
Ministry of Science and Technology (MoST, China)2022YFC2302900 China
CitationJournal: Heliyon / Year: 2024
Title: Structures of SenB and SenA enzymes from Variovorax paradoxus provide insights into carbon-selenium bond formation in selenoneine biosynthesis.
Authors: Xu, S. / Zhao, J. / Liu, X. / Yang, X. / Xu, Z. / Gao, Y. / Ma, Y. / Yang, H.
History
DepositionFeb 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 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.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
A: TIGR04348 family glycosyltransferase
B: TIGR04348 family glycosyltransferase
C: TIGR04348 family glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7986
Polymers105,9763
Non-polymers1,8223
Water3,243180
1
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
2
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
3
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
Unit cell
Length a, b, c (Å)107.898, 56.323, 108.045
Angle α, β, γ (deg.)90.00, 90.94, 90.00
Int Tables number4
Space group name H-MP1211

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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 BL21(DE3) (bacteria) / References: UniProt: A0A952K6X5
#2: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


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.: 180 / Source method: isolated from a natural source / Formula: H2O
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: 3.1 Å3/Da / Density % sol: 60.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 50 mM magnesium sulfate hydrate, 50 mM HEPES sodium pH 7.0, and 1.6 M lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Oct 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.15→49.87 Å / Num. obs: 71180 / % possible obs: 99.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.2
Reflection shellResolution: 2.15→2.18 Å / Rmerge(I) obs: 0.96 / Num. unique obs: 2762

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
HKL-3000data collection
Cootmodel building
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→48.62 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2856 3635 5.11 %
Rwork0.2367 --
obs0.2392 71108 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7239 0 117 180 7536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087534
X-RAY DIFFRACTIONf_angle_d1.02410264
X-RAY DIFFRACTIONf_dihedral_angle_d11.1671076
X-RAY DIFFRACTIONf_chiral_restr0.0521164
X-RAY DIFFRACTIONf_plane_restr0.0091352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.180.30271470.22752615X-RAY DIFFRACTION100
2.18-2.210.27651080.22532595X-RAY DIFFRACTION100
2.21-2.240.25781470.22532552X-RAY DIFFRACTION100
2.24-2.270.29321170.21842579X-RAY DIFFRACTION100
2.27-2.310.26911330.21432596X-RAY DIFFRACTION100
2.31-2.350.25931320.21522618X-RAY DIFFRACTION100
2.35-2.390.2621170.21292587X-RAY DIFFRACTION100
2.39-2.430.27581600.21582544X-RAY DIFFRACTION100
2.43-2.480.30691640.2282564X-RAY DIFFRACTION100
2.48-2.530.30851050.24482608X-RAY DIFFRACTION100
2.53-2.580.28931340.24752574X-RAY DIFFRACTION100
2.58-2.640.31731750.24362570X-RAY DIFFRACTION100
2.64-2.710.28561470.24052575X-RAY DIFFRACTION100
2.71-2.780.31011450.24452554X-RAY DIFFRACTION100
2.78-2.860.35461230.27412606X-RAY DIFFRACTION100
2.86-2.960.32971460.28862604X-RAY DIFFRACTION100
2.96-3.060.38051400.2992557X-RAY DIFFRACTION100
3.06-3.180.31521460.30472621X-RAY DIFFRACTION100
3.18-3.330.39821540.29152570X-RAY DIFFRACTION100
3.33-3.50.34961320.27772612X-RAY DIFFRACTION100
3.5-3.720.28581410.25252631X-RAY DIFFRACTION100
3.72-4.010.26171490.23732590X-RAY DIFFRACTION100
4.01-4.420.23791310.20742597X-RAY DIFFRACTION100
4.42-5.050.2451500.19282647X-RAY DIFFRACTION100
5.05-6.360.26251280.21412670X-RAY DIFFRACTION100
6.37-48.620.20291640.18282637X-RAY DIFFRACTION98

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