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- PDB-8k5u: Se-glycosyltransferase RsSenB -

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Basic information

Entry
Database: PDB / ID: 8k5u
TitleSe-glycosyltransferase RsSenB
ComponentsSe glycosyltransferase
KeywordsTRANSFERASE / Apo
Biological speciesRamlibacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHuang, W. / Long, F.
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
DepositionJul 24, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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: Se glycosyltransferase
B: Se glycosyltransferase


Theoretical massNumber of molelcules
Total (without water)70,3802
Polymers70,3802
Non-polymers00
Water4,666259
1
A: Se glycosyltransferase


Theoretical massNumber of molelcules
Total (without water)35,1901
Polymers35,1901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Se glycosyltransferase


Theoretical massNumber of molelcules
Total (without water)35,1901
Polymers35,1901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.826, 73.790, 81.280
Angle α, β, γ (deg.)90.00, 116.11, 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 Se glycosyltransferase


Mass: 35190.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ramlibacter sp. (bacteria) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.09 Å3/Da / Density % sol: 60.23 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium citrate dibasic 20% PEG 3350

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Data collection

DiffractionMean temperature: 193.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.15→40.54 Å / Num. obs: 46832 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 22.13 Å2 / CC1/2: 0.995 / Net I/σ(I): 9.6
Reflection shellResolution: 2.15→2.22 Å / Num. unique obs: 4046 / CC1/2: 0.802

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Blu-Ice(1.19.2_4158: ???)data collection
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→40.54 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2516 1994 4.26 %
Rwork0.2157 --
obs0.2172 46789 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→40.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4792 0 0 259 5051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084888
X-RAY DIFFRACTIONf_angle_d0.9066654
X-RAY DIFFRACTIONf_dihedral_angle_d6.107695
X-RAY DIFFRACTIONf_chiral_restr0.051763
X-RAY DIFFRACTIONf_plane_restr0.009882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.31531400.25993172X-RAY DIFFRACTION100
2.2-2.260.25341400.24313192X-RAY DIFFRACTION100
2.26-2.330.27841350.22693198X-RAY DIFFRACTION100
2.33-2.410.25721560.23623170X-RAY DIFFRACTION100
2.41-2.490.30491200.23353177X-RAY DIFFRACTION100
2.49-2.590.28591570.22713193X-RAY DIFFRACTION100
2.59-2.710.26261540.22533181X-RAY DIFFRACTION100
2.71-2.850.25511410.2233189X-RAY DIFFRACTION100
2.85-3.030.26591360.22733199X-RAY DIFFRACTION100
3.03-3.260.24311410.22173200X-RAY DIFFRACTION100
3.26-3.590.27721480.21083191X-RAY DIFFRACTION100
3.59-4.110.20721440.19363222X-RAY DIFFRACTION100
4.11-5.180.22491410.18783235X-RAY DIFFRACTION100
5.18-40.540.23011410.21163276X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 20.2861 Å / Origin y: 51.1881 Å / Origin z: 7.3724 Å
111213212223313233
T0.1588 Å2-0.0278 Å20.0014 Å2-0.1799 Å20.0011 Å2--0.1958 Å2
L0.1502 °2-0.149 °2-0.0138 °2-0.3077 °20.0063 °2--0.1069 °2
S0.0171 Å °0.007 Å °0.0137 Å °-0.0332 Å °-0.015 Å °-0.0115 Å °0.0026 Å °-0.0095 Å °-0.0026 Å °
Refinement TLS groupSelection details: all

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