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- PDB-9khu: O-glycosyltransferase from Schisandra chinensis -

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Basic information

Entry
Database: PDB / ID: 9khu
TitleO-glycosyltransferase from Schisandra chinensis
ComponentsGT
KeywordsPLANT PROTEIN / glycosyltransferase
Function / homologyURIDINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesSchisandra chinensis (Chinese magnolia-vine)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBin, L. / Bin, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: O-glycosyltransferase from Schisandra chinensis
Authors: Bin, L.
History
DepositionNov 11, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7113
Polymers51,2141
Non-polymers4962
Water4,504250
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.366, 83.422, 93.028
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GT


Mass: 51214.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schisandra chinensis (Chinese magnolia-vine)
Production host: Escherichia coli (E. coli)
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.06 Å3/Da / Density % sol: 40.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 25% PEG 3350, 0.1 M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Dec 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→12.8 Å / Num. obs: 21989 / % possible obs: 99.4 % / Redundancy: 5.8 % / CC1/2: 0.983 / Rmerge(I) obs: 0.136 / Net I/σ(I): 7.6
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 1996 / CC1/2: 0.911

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
PDB_EXTRACT4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→12.8 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2483 1999 9.12 %
Rwork0.1837 --
obs0.1897 21912 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→12.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3369 0 31 250 3650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083479
X-RAY DIFFRACTIONf_angle_d0.9124730
X-RAY DIFFRACTIONf_dihedral_angle_d8.6392075
X-RAY DIFFRACTIONf_chiral_restr0.049538
X-RAY DIFFRACTIONf_plane_restr0.006598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.25480.281400.19281390X-RAY DIFFRACTION100
2.2548-2.31540.28451400.19491407X-RAY DIFFRACTION100
2.3154-2.38310.30241410.18661391X-RAY DIFFRACTION100
2.3831-2.45950.28391420.18871416X-RAY DIFFRACTION100
2.4595-2.54680.24711400.17741398X-RAY DIFFRACTION100
2.5468-2.64790.23471410.18841405X-RAY DIFFRACTION100
2.6479-2.76720.28841420.19791420X-RAY DIFFRACTION100
2.7672-2.91150.27341410.20521413X-RAY DIFFRACTION99
2.9115-3.09150.25941420.20641414X-RAY DIFFRACTION100
3.0915-3.32630.25021440.18351427X-RAY DIFFRACTION100
3.3263-3.6540.21991430.17571429X-RAY DIFFRACTION100
3.654-4.16670.21621460.16361444X-RAY DIFFRACTION100
4.1667-5.19060.23561450.16141451X-RAY DIFFRACTION100
5.1906-12.80.22031520.19331508X-RAY DIFFRACTION99

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