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- PDB-4x1t: The crystal structure of Arabidopsis thaliana galactolipid syntha... -

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Basic information

Entry
Database: PDB / ID: 4x1t
TitleThe crystal structure of Arabidopsis thaliana galactolipid synthase MGD1 in complex with UDP
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 / chloroplast inner membrane / thylakoid membrane organization / 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
URIDINE-5'-DIPHOSPHATE / Monogalactosyldiacylglycerol synthase 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsRocha, J. / Breton, C.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-10-BLANC-1524 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 25, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 2.0Aug 30, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations
Category: atom_site / diffrn_radiation_wavelength ...atom_site / diffrn_radiation_wavelength / pdbx_audit_support / pdbx_validate_close_contact / struct_site_gen
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 / _struct_site_gen.auth_seq_id
Revision 2.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,29711
Polymers45,3341
Non-polymers96310
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint13 kcal/mol
Surface area14480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.250, 139.250, 38.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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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: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 15-18% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.25→45.58 Å / Num. obs: 20423 / % possible obs: 99.6 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.042 / Rsym value: 0.046 / Net I/σ(I): 20.8
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.9 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WYI

4wyi


Resolution: 2.25→45.58 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.28 / Phase error: 21.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2165 1978 5.13 %random selection
Rwork0.1985 ---
obs0.1994 20419 97.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→45.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2465 0 61 57 2583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072573
X-RAY DIFFRACTIONf_angle_d0.9763458
X-RAY DIFFRACTIONf_dihedral_angle_d16.632983
X-RAY DIFFRACTIONf_chiral_restr0.047393
X-RAY DIFFRACTIONf_plane_restr0.004434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.30630.26991340.28792567X-RAY DIFFRACTION98
2.3063-2.36860.23541520.25592669X-RAY DIFFRACTION98
2.3686-2.43830.28131510.24532590X-RAY DIFFRACTION99
2.4383-2.5170.25121730.2312590X-RAY DIFFRACTION99
2.517-2.6070.25381530.23592579X-RAY DIFFRACTION97
2.607-2.71130.23641200.22332657X-RAY DIFFRACTION98
2.7113-2.83470.26861190.22732646X-RAY DIFFRACTION98
2.8347-2.98410.25811490.21892583X-RAY DIFFRACTION98
2.9841-3.17110.27111490.2222643X-RAY DIFFRACTION98
3.1711-3.41580.21951530.20832559X-RAY DIFFRACTION98
3.4158-3.75940.23761480.18172623X-RAY DIFFRACTION98
3.7594-4.30310.13691280.16982609X-RAY DIFFRACTION98
4.3031-5.420.19511200.16362636X-RAY DIFFRACTION98
5.42-45.58960.21021290.20212617X-RAY DIFFRACTION98
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)
13.11450.25251.01143.06070.24632.79750.4234-0.217-0.70820.1531-0.1966-1.76140.16620.4522-0.17090.6428-0.1160.07520.4810.18451.2881-36.433227.444710.3315
22.81171.46750.41575.90730.73662.75820.01080.2644-0.065-0.5524-0.0426-0.3885-0.11460.22840.04450.38920.02520.07610.1663-0.01650.1884-62.247812.41226.3051
33.02060.4958-0.13342.88080.65821.84430.3830.52990.9285-0.3388-0.0315-0.2209-0.5883-0.037-0.15530.67390.01170.1834-0.0380.0460.4357-56.540626.87486.6476
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 142 through 324 )
2X-RAY DIFFRACTION2chain 'A' and (resid 325 through 474 )
3X-RAY DIFFRACTION3chain 'A' and (resid 475 through 525 )

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