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- EMDB-71210: PDX in Cell-Free Lysate with 300 kDa MWCO Filtration -

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Basic information

Entry
Database: EMDB / ID: EMD-71210
TitlePDX in Cell-Free Lysate with 300 kDa MWCO Filtration
Map dataPDX in Cell-Free Lysate with 300 kDa MWCO Filtration
Sample
  • Complex: PDX
  • Protein or peptide: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
KeywordsPseudoenzyme / PLANT PROTEIN
Function / homology
Function and homology information


amine-lyase activity / pyridoxal 5'-phosphate biosynthetic process / pyridoxine biosynthetic process / amino acid metabolic process / protein heterodimerization activity / cytosol
Similarity search - Function
Pyridoxal 5'-phosphate synthase subunit PdxS/SNZ / PdxS/SNZ N-terminal domain / SOR/SNZ family / PdxS/SNZ family signature. / PdxS/SNZ family profile. / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.37 Å
AuthorsPowell SM / Evans JE
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)EMSL S&T 60672 United States
CitationJournal: To Be Published
Title: Cryo-EM protein structure without purification
Authors: Powell SM / Evans JE
History
DepositionJun 12, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71210.png

Downloads & links

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Map

FileDownload / File: emd_71210.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPDX in Cell-Free Lysate with 300 kDa MWCO Filtration
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 400 pix.
= 336. Å		0.84 Å/pix.
x 400 pix.
= 336. Å		0.84 Å/pix.
x 400 pix.
= 336. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.9082941 - 1.6738989
Average (Standard dev.)-0.0007147168 (±0.049830128)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71210_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Additional Map

Fileemd_71210_additional_1.map
AnnotationAdditional Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_71210_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_71210_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PDX

EntireName: PDX
Components
  • Complex: PDX
  • Protein or peptide: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2

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Supramolecule #1: PDX

SupramoleculeName: PDX / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 448 KDa

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Macromolecule #1: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2

MacromoleculeName: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
SequenceString: MADQAMTDQD QGAVTLYSGT AITDAKKNHP FSVKVGLAQV LRGGAIVEVS SVNQAKLAES AGACSVIVSD PVRSRGGVRR MPDPVLIKEV KRAVSVPVMA RARVGHFVEA QILESLAVDY IDESEIISVA DDDHFINKHN FRSPFICGCR DTGEALRRIR EGAAMIRIQG ...String:
MADQAMTDQD QGAVTLYSGT AITDAKKNHP FSVKVGLAQV LRGGAIVEVS SVNQAKLAES AGACSVIVSD PVRSRGGVRR MPDPVLIKEV KRAVSVPVMA RARVGHFVEA QILESLAVDY IDESEIISVA DDDHFINKHN FRSPFICGCR DTGEALRRIR EGAAMIRIQG DLTATGNIAE TVKNVRSLMG EVRVLNNMDD DEVFTFAKKI SAPYDLVAQT KQMGRVPVVQ FASGGITTPA DAALMMQLGC DGVFVGSEVF DGPDPFKKLR SIVQAVQHYN DPHVLAEMSS GLENAMESLN VRGDRIQDFG QGSV

UniProtKB: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2

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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

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS 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: 1.3 µm / Nominal defocus min: 0.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.37 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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