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- EMDB-53095: Cryo-EM structure of apo form of Arthrobacter psychrolactophilus ... -

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Basic information

Entry
Database: EMDB / ID: EMD-53095
TitleCryo-EM structure of apo form of Arthrobacter psychrolactophilus L-arabinose isomerase
Map data
Sample
  • Complex: Homo 6-mer of L-arabinose isomerase
    • Protein or peptide: L-arabinose isomerase
KeywordsIsomerase / Apo form / enzyme
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.52 Å
AuthorsLaksmi FA / Jayawardena N / Nugraha Y / Raschdorf O / Herliana L / Hidayat I / Kohga H / Fey CM
Funding supportIndonesia, 2 items
OrganizationGrant numberCountry
Other governmentNKB-507/UN2.RST/HKP.05.00/2024Indonesia
Other government1/III.5/ HK/2024Indonesia
CitationJournal: To Be Published
Title: Cryo-EM structure of apo form of E.coli L-arabinose isomerase
Authors: Laksmi FA / Jayawardena N / Nugraha Y / Raschdorf O / Herliana L / Hidayat I
History
DepositionMar 11, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53095.png

Downloads & links

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Map

FileDownload / File: emd_53095.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 512 pix.
= 293.376 Å		0.57 Å/pix.
x 512 pix.
= 293.376 Å		0.57 Å/pix.
x 512 pix.
= 293.376 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.573 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0865
Minimum - Maximum-0.48167 - 1.0537609
Average (Standard dev.)0.00011286633 (±0.016434412)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 293.376 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53095_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53095_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53095_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Sample components

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Entire : Homo 6-mer of L-arabinose isomerase

EntireName: Homo 6-mer of L-arabinose isomerase
Components
  • Complex: Homo 6-mer of L-arabinose isomerase
    • Protein or peptide: L-arabinose isomerase

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Supramolecule #1: Homo 6-mer of L-arabinose isomerase

SupramoleculeName: Homo 6-mer of L-arabinose isomerase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 168 KDa

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Macromolecule #1: L-arabinose isomerase

MacromoleculeName: L-arabinose isomerase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: LNNSLSEYEV WFLTGSQNLY GEETLRQVAE QSAEVAKTLQ ESTEIPVRVV FKDVLKDSES IRRAALDAN ADNKVIGLIA WMHTFSPAKM WIRGLSELNK PLLHLHTQAN VALPWAEIDF D FMNLNQAA HGDREFGYMQ SRMGISRKTV VGHVSNPLVR EKIGTWTRAA ...String:
LNNSLSEYEV WFLTGSQNLY GEETLRQVAE QSAEVAKTLQ ESTEIPVRVV FKDVLKDSES IRRAALDAN ADNKVIGLIA WMHTFSPAKM WIRGLSELNK PLLHLHTQAN VALPWAEIDF D FMNLNQAA HGDREFGYMQ SRMGISRKTV VGHVSNPLVR EKIGTWTRAA SAVAQIRTLK VA RFGDNMR NVAVTEGDKT EAEIRFGVSV NSWSVNELAE AVDAASEADV DVLIAEYLRL YNV APELLP GAARHDSLRY GAKIELGLRS FLEAGDFGAF TTNFEDLGGL RQLPGLAVQR LMAD GYGFG AEGDWKTAIL IRAAKVMGEG LPGGASLMED YTYHLVPGQE KILGAHMLEV CPSLT TAKP SLEVHPLGIG GREDPVRLVF DADPGAGVVV ALSDMRERFR LTANKVEVVP LDEPLP NLP VARAVWKPLP DFATSAAAWL EAGAAHHTVM STAVGIEAFQ DFADIFEAEL LVIDEDT TQ RGFVREIRWN QAYYRLAQGF

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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

Concentration10 mg/mL
BufferpH: 8 / Details: 50 mM Tris-HCl buffer with a pH of 8.0.
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 215000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 1.52 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 1732769
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

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