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- EMDB-38558: The structure determination of prokaryotic Glycerol-3-phosphate A... -

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Basic information

Entry
Database: EMDB / ID: EMD-38558
TitleThe structure determination of prokaryotic Glycerol-3-phosphate Acyltransferase
Map data
Sample
  • Complex: PlsB, Palmitoyl CoA, 1,2-dioleoyl-sn-glycero-3-phosphate
    • Protein or peptide: PlsB from Themomonas haemolytica (ThPlsB)
Keywordsenzyme on the membrane / de newo synthetase of phospholipid / complex of enzyme ang ligands / LIPID TRANSPORT
Biological speciesThermomonas haemolytica (bacteria)
Methodsingle particle reconstruction / Resolution: 2.79 Å
AuthorsLi YM / Liu ZF
Funding support China, 1 items
OrganizationGrant numberCountry
Other private China
CitationJournal: To Be Published
Title: The phospholipid biosynthesis enzyme PlsB contains three distinct domains for membrane association, lysophosphatidic acid synthesis and dimerization
Authors: Li YM / Liu ZF
History
DepositionJan 4, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38558.png

Downloads & links

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Map

FileDownload / File: emd_38558.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0314
Minimum - Maximum-0.12162754 - 0.2349384
Average (Standard dev.)0.00012973692 (±0.003644256)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38558_msk_1.map
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Half map: #2

Fileemd_38558_half_map_1.map
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Half map: #1

Fileemd_38558_half_map_2.map
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Sample components

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Entire : PlsB, Palmitoyl CoA, 1,2-dioleoyl-sn-glycero-3-phosphate

EntireName: PlsB, Palmitoyl CoA, 1,2-dioleoyl-sn-glycero-3-phosphate
Components
  • Complex: PlsB, Palmitoyl CoA, 1,2-dioleoyl-sn-glycero-3-phosphate
    • Protein or peptide: PlsB from Themomonas haemolytica (ThPlsB)

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Supramolecule #1: PlsB, Palmitoyl CoA, 1,2-dioleoyl-sn-glycero-3-phosphate

SupramoleculeName: PlsB, Palmitoyl CoA, 1,2-dioleoyl-sn-glycero-3-phosphate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: PlsB is a crucial enzyme catalyzing the first step of phospholipid synthesis by converting glycerol-3-phosphate and fatty acyl-coenzyme A (CoA)/acyl-carrier protein (ACP) to lysophosphatidic ...Details: PlsB is a crucial enzyme catalyzing the first step of phospholipid synthesis by converting glycerol-3-phosphate and fatty acyl-coenzyme A (CoA)/acyl-carrier protein (ACP) to lysophosphatidic acid and free CoA (CoASH)/ACP.
Source (natural)Organism: Thermomonas haemolytica (bacteria)

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Macromolecule #1: PlsB from Themomonas haemolytica (ThPlsB)

MacromoleculeName: PlsB from Themomonas haemolytica (ThPlsB) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: glycerol-3-phosphate 1-O-acyltransferase
Source (natural)Organism: Thermomonas haemolytica (bacteria) / Strain: Thermomonas haemolytica
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAAMPDRHSP DQPGLFDPPA AADDAATGPA GPAPLPLPGF LAADAATPPG PPSPPPAGKA RNPLWARLLG RLLAPWLRLE IEVDPAIAAD PRPICYVLED YGLSNALILQ RACREAALPP PLQPIAGDPL GRRRAYVALS RRHVNALGLL PGAEHKTHSG SLARLLQAHQ ...String:
MAAMPDRHSP DQPGLFDPPA AADDAATGPA GPAPLPLPGF LAADAATPPG PPSPPPAGKA RNPLWARLLG RLLAPWLRLE IEVDPAIAAD PRPICYVLED YGLSNALILQ RACREAALPP PLQPIAGDPL GRRRAYVALS RRHVNALGLL PGAEHKTHSG SLARLLQAHQ QQPELDVHLV PVSIFVGQAP KRSSGWFSVL FSENWTLVGR FRRLLAILLN GRDTLVKFAA PVPVREIVAE GLEPERTVRK LSRILRTHFR RVREVVIGPD LSTRRMLADQ VLSSPLVKEA IADQARRDGS KPEAAWEKAN AYFWEIAADY SNTVVRSASF ALTFVWNRIY RGVLVHHLDQ FKQEAPGHEV VYVPSHRSHM DYLLVSYLLY THGVVPPHIF AGINLNLPVV GTLLRKGGAF FARRSFKGNA LYSAVFREYM AQLVAGGYSI EYFIEGGRSR TGRLLQPKGG SLAMTVRAYL RQPTRPVLFQ PVYIGYEKLM EGRSYLDELS GKPKEKESIW QLLAGIPKVL RSNYGQVVVN FGERIQLSQV LAELAPEWDG QPIGDDEKPA WFARTVDALA QRIQTNVNRA ADVNPINLLA LALLSTPKHA MGEADLRAQI ALSKTLLAEV PYSDWVTVTP HTPEQIIAHG EEIGLITRTA HPLGDVLGVE GDNAVLLSYF RNNVLHLFTA SSWIAVCFQN NRRMGRRQLQ QIGRTLYPFL QAELFLPWDE ETFAARIDRT IEVFVREGLL EQVSDEDGGI LQRNAGQSDE VFRLRALGHT LQQAFERYYI AIAILVKNGS GTLQAGELES LCQLTAQRLS LLYAPAAPEF FDKTLFRGFI QKLRELKLVW PDDTGRLAFD ERLKAWAKDA RVVLGRELRH TIEKISPAGS GRSSGEQPAL PPDPAATNGA S

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration6 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
500.0 mMNaClsodium chloride
2.0 mMDTTDithiothreitol
5.0 mMEDTAEthylenediaminetetraacetic acid
0.1 %GDNGlyco-diosgenin

Details: 500 mM KCl, 2 mM DTT, 5 mM EDTA and 0.1% GDN
Sugar embeddingMaterial: GDN
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR
DetailsThe specimen was purified through Ni-TNA, and incubated overnight with the substrate. The secondary purification was performed by size-exclusion chromatography.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 91865
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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