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- PDB-8p6s: Arabidopsis thaliana DGD2 in complex with UDP-galactose -

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Basic information

Entry
Database: PDB / ID: 8p6s
TitleArabidopsis thaliana DGD2 in complex with UDP-galactose
ComponentsDigalactosyldiacylglycerol synthase 2, chloroplastic
KeywordsTRANSFERASE / glycosyltransferase / substrate
Function / homology
Function and homology information


digalactosyldiacylglycerol synthase / digalactosyldiacylglycerol synthase activity / chloroplast outer membrane / UDP-galactosyltransferase activity / glycolipid biosynthetic process / UDP-glycosyltransferase activity / cellular response to phosphate starvation
Similarity search - Function
Digalactosyldiacylglycerol synthase 1/2 / Glycosyl transferase, family 1 / Glycosyl transferases group 1
Similarity search - Domain/homology
GALACTOSE-URIDINE-5'-DIPHOSPHATE / Digalactosyldiacylglycerol synthase 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsScaletti, E.R. / Martinez-Carranza, M. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Structure and membrane interactions of Arabidopsis thaliana DGD2, a glycosyltransferase in the chloroplast membrane.
Authors: Scaletti Hutchinson, E. / Martinez-Carranza, M. / Fu, B. / Maler, L. / Stenmark, P.
History
DepositionMay 29, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: Database references / Category: citation / citation_author
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Digalactosyldiacylglycerol synthase 2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2272
Polymers47,6601
Non-polymers5661
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.032, 44.032, 368.478
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Digalactosyldiacylglycerol synthase 2, chloroplastic


Mass: 47660.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DGD2, At4g00550, F6N23.24 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8W1S1, digalactosyldiacylglycerol synthase
#2: Chemical ChemComp-GDU / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-D-GALACTOPYRANOSE


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.03 Å3/Da / Density % sol: 39.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M bicine/Trizma base pH 8.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02M 1,3-Propanediol, 0.02M 1,4-Butanediol, 0.02M 1,6-Hexanediol, 0.02M 1-Butanol, 0.02M 2-Propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→92.29 Å / Num. obs: 22546 / % possible obs: 99.1 % / Redundancy: 58 % / CC1/2: 1 / Net I/σ(I): 20.5
Reflection shellResolution: 2.1→2.16 Å / Num. unique obs: 1576 / CC1/2: 0.488

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
DIALSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→92.29 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 13.236 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25658 1154 5.2 %RANDOM
Rwork0.20325 ---
obs0.2061 21090 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.626 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20 Å2
2--0.86 Å2-0 Å2
3----1.71 Å2
Refinement stepCycle: 1 / Resolution: 2.1→92.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2937 0 36 60 3033
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0123044
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162819
X-RAY DIFFRACTIONr_angle_refined_deg2.2111.6534144
X-RAY DIFFRACTIONr_angle_other_deg0.7051.5726472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3435373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.625515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.49910488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1040.2472
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023501
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02700
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.3243.3361501
X-RAY DIFFRACTIONr_mcbond_other4.3253.3361501
X-RAY DIFFRACTIONr_mcangle_it5.8085.9671871
X-RAY DIFFRACTIONr_mcangle_other5.8095.9681872
X-RAY DIFFRACTIONr_scbond_it6.0323.7091543
X-RAY DIFFRACTIONr_scbond_other6.0363.7111544
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.2726.612274
X-RAY DIFFRACTIONr_long_range_B_refined9.8133.983412
X-RAY DIFFRACTIONr_long_range_B_other9.80233.983409
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 75 -
Rwork0.294 1327 -
obs--88.62 %
Refinement TLS params.Method: refined / Origin x: 6.948 Å / Origin y: -4.075 Å / Origin z: 25.246 Å
111213212223313233
T0.091 Å2-0.0039 Å2-0.0287 Å2-0.0269 Å2-0.0094 Å2--0.0886 Å2
L2.2251 °20.3648 °2-0.667 °2-2.4841 °2-0.3708 °2--2.7307 °2
S-0.0584 Å °0.2311 Å °-0.0699 Å °-0.3984 Å °-0.0128 Å °0.0392 Å °0.2732 Å °-0.1315 Å °0.0712 Å °

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