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- PDB-4wyi: The crystal structure of Arabidopsis thaliana galactolipid syntha... -

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Basic information

Entry
Database: PDB / ID: 4wyi
TitleThe crystal structure of Arabidopsis thaliana galactolipid synthase, MGD1 (apo-form)
ComponentsMonogalactosyldiacylglycerol synthase 1, chloroplastic
KeywordsTRANSFERASE / monogalactosyldiacylglycerol synthase / GT-B fold / Glycosyltransferase / Galactolipid
Function / homology
Function and homology information


monogalactosyldiacylglycerol synthase / 1,2-diacylglycerol 3-beta-galactosyltransferase activity / thylakoid membrane organization / chloroplast inner membrane / UDP-galactosyltransferase activity / glycolipid biosynthetic process / UDP-glycosyltransferase activity / embryo development ending in seed dormancy / chloroplast envelope / plastid / plasma membrane
Similarity search - Function
Diacylglycerol glucosyltransferase, N-terminal / : / Monogalactosyldiacylglycerol (MGDG) synthase / Glycosyl transferase, family 28, C-terminal / Glycosyltransferase family 28 C-terminal domain
Similarity search - Domain/homology
Monogalactosyldiacylglycerol synthase 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRocha, J. / Breton, C.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: Plant J. / Year: 2016
Title: Structural insights and membrane binding properties of MGD1, the major galactolipid synthase in plants.
Authors: Rocha, J. / Sarkis, J. / Thomas, A. / Pitou, L. / Radzimanowski, J. / Audry, M. / Chazalet, V. / de Sanctis, D. / Palcic, M.M. / Block, M.A. / Girard-Egrot, A. / Marechal, E. / Breton, C.
History
DepositionNov 17, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 2.0Aug 30, 2017Group: Advisory / Atomic model / Author supporting evidence
Category: atom_site / pdbx_audit_support / pdbx_validate_close_contact
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_validate_close_contact.auth_seq_id_2
Revision 2.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Monogalactosyldiacylglycerol synthase 1, chloroplastic


Theoretical massNumber of molelcules
Total (without water)45,3341
Polymers45,3341
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.610, 65.619, 80.401
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 Monogalactosyldiacylglycerol synthase 1, chloroplastic / AtMGD1 / MGDG synthase type A


Mass: 45333.730 Da / Num. of mol.: 1 / Fragment: UNP residues 137-533
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MGD1, MGDA, At4g31780, F28M20.30 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O81770, monogalactosyldiacylglycerol synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.79 Å3/Da / Density % sol: 31.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M magnesium chloride, 22% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9811 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9811 Å / Relative weight: 1
ReflectionResolution: 2.5→47.53 Å / Num. obs: 11358 / % possible obs: 99.5 % / Redundancy: 4.8 % / Biso Wilson estimate: 41.51 Å2 / Net I/σ(I): 14.3
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 4.1 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→32.81 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0.9 / Phase error: 21.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1999 983 4.78 %random selection
Rwork0.1806 ---
obs0.1815 11314 97.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.33 Å2
Refinement stepCycle: LAST / Resolution: 2.5→32.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2589 0 0 36 2625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0232636
X-RAY DIFFRACTIONf_angle_d1.4133554
X-RAY DIFFRACTIONf_dihedral_angle_d18.0771010
X-RAY DIFFRACTIONf_chiral_restr0.13406
X-RAY DIFFRACTIONf_plane_restr0.012452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5003-2.6320.32261350.25682821X-RAY DIFFRACTION98
2.632-2.79690.22421460.23952828X-RAY DIFFRACTION98
2.7969-3.01270.24791340.21672788X-RAY DIFFRACTION98
3.0127-3.31560.22851490.20112825X-RAY DIFFRACTION98
3.3156-3.79470.17371410.16722788X-RAY DIFFRACTION97
3.7947-4.77860.17141170.13982789X-RAY DIFFRACTION96
4.7786-32.81230.18121610.17152750X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3154-0.46490.05272.1852-0.8082.51950.00040.1739-0.1182-0.0426-0.08080.11280.0956-0.27480.03310.2392-0.02470.04170.2223-0.01740.2039-2.109516.336930.3153
21.85050.0574-0.27251.82870.25942.33980.02620.0641-0.0802-0.006-0.07150.00650.0123-0.07590.0370.1655-0.0116-0.00810.1980.02310.190313.613419.05783.5762
32.63531.4241-2.7232.2169-2.07574.66180.2601-0.4351-0.06410.2626-0.22870.0708-0.1630.52160.03960.26030.0118-0.06370.2468-0.00470.273214.621819.91626.8472
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 140 through 333 )
2X-RAY DIFFRACTION2chain 'A' and (resid 334 through 489 )
3X-RAY DIFFRACTION3chain 'A' and (resid 490 through 523 )

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