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- EMDB-33209: AhCS-3Mg2+-FSPP -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-33209
TitleAhCS-3Mg2+-FSPP
Map data
Sample
  • Complex: AhCS-3Mg2+-FSPP
  • Protein or peptide: (-)-cyperene synthase
Keywords(-)-cyperene synthase / directed evolution / Alphafold2 / PLANT PROTEIN
Biological speciesArtabotrys hexapetalus (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsYu SS / Zhu P / Liu YB / Ma SG / Ye D / Shao YZ / Li WR / Cui ZJ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21732008 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Characterisation and engineering of two highly paralogous sesquiterpene synthases reveal a regioselective reprotonation switch.
Authors: Ye D / Shao YZ / Li WR / Cui ZJ / Gong T / Yang JL / Wang HQ / Dai JG / Feng KP / Ma M / Ma SG / Liu YB / Zhu P / Yu SS
History
DepositionApr 14, 2022-
Header (metadata) releaseOct 18, 2023-
Map releaseOct 18, 2023-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33209.png

Downloads & links

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Map

FileDownload / File: emd_33209.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 240 pix.
= 194.4 Å		0.81 Å/pix.
x 240 pix.
= 194.4 Å		0.81 Å/pix.
x 240 pix.
= 194.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.647
Minimum - Maximum-3.2979345 - 4.372386
Average (Standard dev.)-0.0002771305 (±0.104261965)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 194.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : AhCS-3Mg2+-FSPP

EntireName: AhCS-3Mg2+-FSPP
Components
  • Complex: AhCS-3Mg2+-FSPP
  • Protein or peptide: (-)-cyperene synthase

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Supramolecule #1: AhCS-3Mg2+-FSPP

SupramoleculeName: AhCS-3Mg2+-FSPP / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Artabotrys hexapetalus (plant)

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Macromolecule #1: (-)-cyperene synthase

MacromoleculeName: (-)-cyperene synthase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Artabotrys hexapetalus (plant)
Recombinant expressionOrganism: Escherichia coli B (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MMGRSSANFH PNVWGDRFVM MPSKEMETDA STKQRAEMLK QEVKKMLHDV SGSLQELNLI NEIQRLGVAY HFEAEISNAL ERIYNREKNE NGINDCDLHA VALRFRLLRQ HGYNVSSDVF KKFKDENGEF EARFRNDVRG LLSLYEAAYF ...String:
MGSSHHHHHH SSGLVPRGSH MMGRSSANFH PNVWGDRFVM MPSKEMETDA STKQRAEMLK QEVKKMLHDV SGSLQELNLI NEIQRLGVAY HFEAEISNAL ERIYNREKNE NGINDCDLHA VALRFRLLRQ HGYNVSSDVF KKFKDENGEF EARFRNDVRG LLSLYEAAYF GTQEDGHLDE AIAFTTKHLK SLLPHLSSPL SDLVKLALDL PLLKRIERLQ SKHFISIYQQ DEDRNNVLLE FAKIDFNILQ ALHRKELNEI TRWWNESDLP RKLPFIRDRL VECYIWMLEL YYEPQYSQSR RMTTILLILT SSMDDIYDVY GKLEELERYT VAVERWEREA LDQLPDYMRV HLGVLLTVVE NFEDELGKEG KSFHLAYVKK AFAELTKAYI KEARWANAEH VPALEEYVDN AVVSSAYPLI TTMSLLGMGK VATKEAFEWT ISLPNAVRQC SMICRLVNDI MSNQSEQERV HVASAVQCCM KEFSTTYEEA CKILQEKIAR AWKDLNKECL HPIPVSLELI RRPLNLARAI EFYYQCRDGY SDSAFEIKDY ITMLLVEPAV V

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 283635
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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