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- PDB-7y4i: Crystal structure of SPINDLY in complex with GDP -

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Basic information

Entry
Database: PDB / ID: 7y4i
TitleCrystal structure of SPINDLY in complex with GDP
ComponentsProbable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY
KeywordsTRANSFERASE / O-fucosyltransferase / PLANT PROTEIN
Function / homology
Function and homology information


negative regulation of gibberellic acid mediated signaling pathway / protein N-acetylglucosaminyltransferase activity / peptide-O-fucosyltransferase / gibberellic acid mediated signaling pathway / protein O-linked fucosylation / peptide-O-fucosyltransferase activity / cytokinin-activated signaling pathway / protein O-GlcNAc transferase / protein O-acetylglucosaminyltransferase activity / flower development ...negative regulation of gibberellic acid mediated signaling pathway / protein N-acetylglucosaminyltransferase activity / peptide-O-fucosyltransferase / gibberellic acid mediated signaling pathway / protein O-linked fucosylation / peptide-O-fucosyltransferase activity / cytokinin-activated signaling pathway / protein O-GlcNAc transferase / protein O-acetylglucosaminyltransferase activity / flower development / regulation of reactive oxygen species metabolic process / rhythmic process / cell differentiation / nucleus / cytoplasm
Similarity search - Function
Sel1-like repeat / Sel1-like repeats. / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. ...Sel1-like repeat / Sel1-like repeats. / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsXu, S.T. / Wan, L.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000900 China
CitationJournal: Nat Commun / Year: 2022
Title: Structural insights into mechanism and specificity of the plant protein O-fucosyltransferase SPINDLY.
Authors: Zhu, L. / Wei, X. / Cong, J. / Zou, J. / Wan, L. / Xu, S.
History
DepositionJun 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 3, 2024Group: 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: Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY
B: Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,4993
Polymers203,0562
Non-polymers4431
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-23 kcal/mol
Surface area71430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.735, 130.677, 141.368
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY / GDP-fucose protein O-fucosyltransferase SPINDLY


Mass: 101527.828 Da / Num. of mol.: 2 / Fragment: Glycosyltransferase / Mutation: C645S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SPY, At3g11540, F24K9.29 / Plasmid: pET28sumo / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q96301, protein O-GlcNAc transferase, peptide-O-fucosyltransferase
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 7.5
Details: 0.1 M bicine, 24% Polyethylene glycol 1,500, and 10% (v/v) 2-Propanol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97931 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 65883 / % possible obs: 99.6 % / Redundancy: 13 % / Biso Wilson estimate: 65.68 Å2 / CC1/2: 1 / Net I/σ(I): 8.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 13 % / Num. unique obs: 6457 / CC1/2: 1 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AF2D

Resolution: 2.85→35.34 Å / SU ML: 0.4305 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.0523
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2699 2930 5.27 %
Rwork0.2127 52714 -
obs0.2158 55644 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.93 Å2
Refinement stepCycle: LAST / Resolution: 2.85→35.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12779 0 28 5 12812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003213094
X-RAY DIFFRACTIONf_angle_d0.613117776
X-RAY DIFFRACTIONf_chiral_restr0.04211977
X-RAY DIFFRACTIONf_plane_restr0.00492280
X-RAY DIFFRACTIONf_dihedral_angle_d22.47714787
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.90.39421250.35022471X-RAY DIFFRACTION98.82
2.9-2.950.38221190.33112501X-RAY DIFFRACTION100
2.95-30.381280.32182501X-RAY DIFFRACTION100
3-3.060.3531300.31472481X-RAY DIFFRACTION100
3.06-3.120.36041320.31192524X-RAY DIFFRACTION99.96
3.12-3.190.35141170.29732493X-RAY DIFFRACTION99.96
3.19-3.260.31531440.29782498X-RAY DIFFRACTION99.89
3.26-3.340.3181520.26272471X-RAY DIFFRACTION99.92
3.34-3.430.31381650.23622485X-RAY DIFFRACTION99.96
3.43-3.530.28961640.22362455X-RAY DIFFRACTION99.96
3.54-3.650.25121640.22692485X-RAY DIFFRACTION99.96
3.65-3.780.31361510.22522478X-RAY DIFFRACTION99.96
3.78-3.930.27721450.20192523X-RAY DIFFRACTION99.89
3.93-4.110.26881210.18862517X-RAY DIFFRACTION99.77
4.11-4.330.25641590.16672483X-RAY DIFFRACTION99.85
4.33-4.60.24091440.16862521X-RAY DIFFRACTION99.85
4.6-4.950.22431000.16982586X-RAY DIFFRACTION99.96
4.95-5.450.25841570.19082530X-RAY DIFFRACTION99.85
5.45-6.230.23451260.19022569X-RAY DIFFRACTION99.74
6.23-7.830.23391330.19262567X-RAY DIFFRACTION99.12
7.84-35.340.21551540.16982575X-RAY DIFFRACTION95.39

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