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- PDB-6kqx: Crystal structure of Yijc from B. subtilis in complex with UDP -

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Basic information

Entry
Database: PDB / ID: 6kqx
TitleCrystal structure of Yijc from B. subtilis in complex with UDP
ComponentsUncharacterized UDP-glucosyltransferase YjiC
KeywordsTRANSFERASE / prenyltransferase
Function / homology
Function and homology information


NDP-glycosyltransferase / UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process
Similarity search - Function
UDP-glycosyltransferase, MGT-like / Erythromycin biosynthesis protein CIII-like, central / : / Erythromycin biosynthesis protein CIII-like, C-terminal domain / UDP-glucuronosyl/UDP-glucosyltransferase
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / NDP-glycosyltransferase YjiC
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsHu, Y.M. / Dai, L.H. / Huang, J.W. / Liu, W.D. / Chen, C.C. / Guo, R.T.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Structural dissection of unnatural ginsenoside-biosynthetic UDP-glycosyltransferase Bs-YjiC from Bacillus subtilis for substrate promiscuity.
Authors: Dai, L.H. / Qin, L. / Hu, Y.M. / Huang, J.W. / Hu, Z. / Min, J. / Sun, Y. / Guo, R.T.
History
DepositionAug 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized UDP-glucosyltransferase YjiC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4382
Polymers44,0331
Non-polymers4041
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-9 kcal/mol
Surface area15410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.152, 116.722, 185.226
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Uncharacterized UDP-glucosyltransferase YjiC


Mass: 44033.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: yjiC, BSU12220 / Plasmid: pET-46EK/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O34539, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.2 Å3/Da / Density % sol: 61.57 % / Mosaicity: 1.602 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.2 M tri-Sodium Citrate dehydrate, 0.1 M Bis-Tris Propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 11, 2018
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.44→25 Å / Num. obs: 21112 / % possible obs: 98.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 56.83 Å2 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.029 / Rrim(I) all: 0.058 / Χ2: 1.46 / Net I/σ(I): 15 / Num. measured all: 83151
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.44-2.533.70.52518190.820.2950.6051.26487.5
2.53-2.633.70.4420600.880.2540.5111.24296.8
2.63-2.753.80.34621290.9080.2020.4031.27299.7
2.75-2.893.90.26420990.9570.1530.3071.277100
2.89-3.073.90.16521200.9790.0960.1911.33399.9
3.07-3.313.90.11421260.9890.0650.1311.605100
3.31-3.644.10.07121390.9950.0390.0811.716100
3.64-4.174.30.04121630.9980.0220.0471.529100
4.17-5.244.10.03421720.9980.0190.0391.91799.9
5.24-2540.02522850.9990.0140.0281.31499.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX(1.13_2998: ???)refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IAA

3iaa


Resolution: 2.44→24.688 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.25
RfactorNum. reflection% reflection
Rfree0.26 1056 5.01 %
Rwork0.23 --
obs0.2316 21098 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 167.79 Å2 / Biso mean: 82.0275 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.44→24.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2546 0 25 19 2590
Biso mean--63.07 54.68 -
Num. residues----327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042708
X-RAY DIFFRACTIONf_angle_d0.7553674
X-RAY DIFFRACTIONf_dihedral_angle_d3.441639
X-RAY DIFFRACTIONf_chiral_restr0.048422
X-RAY DIFFRACTIONf_plane_restr0.005475
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4401-2.55110.30311130.28362153226687
2.5511-2.68540.33781310.27962475260698
2.6854-2.85350.32231320.267125192651100
2.8535-3.07340.31021340.249225322666100
3.0734-3.3820.27571330.243325312664100
3.382-3.86980.23191350.218325642699100
3.8698-4.86930.22581360.202625762712100
4.8693-24.68880.26091420.230426922834100

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