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- PDB-8ia1: plastidial glycerol-3-phosphate acyltransferases (GPAT) from the ... -

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Basic information

Entry
Database: PDB / ID: 8ia1
Titleplastidial glycerol-3-phosphate acyltransferases (GPAT) from the green alga Myrmecia incisa
ComponentsGlycerol-3-phosphate acyltransferase, chloroplastic
KeywordsTRANSFERASE / plastidial glycerol-3-phosphate acyltransferases
Function / homology
Function and homology information


glycerol-3-phosphate 1-O-acyltransferase / glycerol-3-phosphate O-acyltransferase activity / : / CDP-diacylglycerol biosynthetic process / chloroplast stroma
Similarity search - Function
Glycerol-3-phosphate O-acyltransferase, chloroplast / Glycerol-3-phosphate O-acyltransferase, alpha helical bundle, N-terminal / GPAT, N-terminal domain superfamily / Glycerol-3-phosphate acyltransferase N-terminal / Phospholipid/glycerol acyltransferase / Acyltransferase / Phosphate acyltransferases / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Glycerol-3-phosphate acyltransferase, chloroplastic
Similarity search - Component
Biological speciesLobosphaera incisa (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsSong, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21877110 China
CitationJournal: To Be Published
Title: Unique recognition of the microalgal plastidial glycerol-3-phosphate acyltransferase for acyl-ACP
Authors: Song, X.
History
DepositionFeb 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycerol-3-phosphate acyltransferase, chloroplastic
B: Glycerol-3-phosphate acyltransferase, chloroplastic
C: Glycerol-3-phosphate acyltransferase, chloroplastic


Theoretical massNumber of molelcules
Total (without water)124,9543
Polymers124,9543
Non-polymers00
Water6,323351
1
A: Glycerol-3-phosphate acyltransferase, chloroplastic


Theoretical massNumber of molelcules
Total (without water)41,6511
Polymers41,6511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycerol-3-phosphate acyltransferase, chloroplastic


Theoretical massNumber of molelcules
Total (without water)41,6511
Polymers41,6511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycerol-3-phosphate acyltransferase, chloroplastic


Theoretical massNumber of molelcules
Total (without water)41,6511
Polymers41,6511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.093, 81.553, 88.489
Angle α, β, γ (deg.)110.847, 106.790, 99.932
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Glycerol-3-phosphate acyltransferase, chloroplastic


Mass: 41651.180 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lobosphaera incisa (plant) / Gene: GPAT / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B5EHP8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2M (NH4)2SO4, 0.1M Tris-HCl pH 8.5, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1.0001 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0001 Å / Relative weight: 1
ReflectionResolution: 2.31→37.32 Å / Num. obs: 50682 / % possible obs: 89.19 % / Redundancy: 2.2 % / Biso Wilson estimate: 28.13 Å2 / CC1/2: 0.99 / Net I/av σ(I): 16.1 / Net I/σ(I): 16.1
Reflection shellResolution: 2.31→2.38 Å / Mean I/σ(I) obs: 2.61 / Num. unique obs: 2902 / CC1/2: 0.76

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000HKL2000_v723-Linuxdata reduction
HKL-2000HKL2000_v723-Linuxdata scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→37.32 Å / SU ML: 0.2843 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 24.9081
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2416 2320 4.85 %
Rwork0.1834 45495 -
obs0.1862 47815 89.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.65 Å2
Refinement stepCycle: LAST / Resolution: 2.31→37.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8565 0 0 351 8916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00768772
X-RAY DIFFRACTIONf_angle_d0.921811913
X-RAY DIFFRACTIONf_chiral_restr0.05041308
X-RAY DIFFRACTIONf_plane_restr0.00611560
X-RAY DIFFRACTIONf_dihedral_angle_d3.04225268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.350.2977820.21781362X-RAY DIFFRACTION45.29
2.35-2.40.30171030.21312006X-RAY DIFFRACTION66.87
2.4-2.460.32511360.21962389X-RAY DIFFRACTION79.91
2.46-2.520.25711370.21532685X-RAY DIFFRACTION90.02
2.52-2.590.29731310.20722897X-RAY DIFFRACTION96.28
2.59-2.670.28011580.212859X-RAY DIFFRACTION96.54
2.67-2.750.23981450.20462917X-RAY DIFFRACTION96.75
2.75-2.850.28561300.20192966X-RAY DIFFRACTION96.93
2.85-2.960.26621470.20562863X-RAY DIFFRACTION96.94
2.96-3.10.25561570.20672869X-RAY DIFFRACTION96.43
3.1-3.260.25681500.20162914X-RAY DIFFRACTION95.72
3.26-3.470.27281430.18292837X-RAY DIFFRACTION95.57
3.47-3.740.21861310.17712867X-RAY DIFFRACTION94.96
3.74-4.110.20461440.16582800X-RAY DIFFRACTION94.21
4.11-4.70.20631600.15362790X-RAY DIFFRACTION92.48
4.7-5.920.22031210.16142751X-RAY DIFFRACTION91.55
5.92-37.320.20941450.15992723X-RAY DIFFRACTION91.13

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