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- EMDB-37598: Cryo-EM structure of a bacterial protein -

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Basic information

Entry
Database: EMDB / ID: EMD-37598
TitleCryo-EM structure of a bacterial protein
Map datamain map
Sample
  • Complex: Cryo-EM structure of a bacterial protein
    • Protein or peptide: bacterial protein
Keywordsbacterial immune proteins / IMMUNE SYSTEM
Biological speciesPaenibacillus sp. 453mf (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsYu G / Liao F / Li X / Li Z / Zhang H
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32200496 China
CitationJournal: To Be Published
Title: Cryo-EM structure of a bacterial protein
Authors: Yu G / Liao F / Li X / Li Z / Zhang H
History
DepositionSep 27, 2023-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37598.png

Downloads & links

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Map

FileDownload / File: emd_37598.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 275.4 Å		1.08 Å/pix.
x 256 pix.
= 275.4 Å		1.08 Å/pix.
x 256 pix.
= 275.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07578 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.6835007 - 0.9919529
Average (Standard dev.)0.00009245392 (±0.02785203)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 275.3997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map

Fileemd_37598_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map

Fileemd_37598_half_map_2.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of a bacterial protein

EntireName: Cryo-EM structure of a bacterial protein
Components
  • Complex: Cryo-EM structure of a bacterial protein
    • Protein or peptide: bacterial protein

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Supramolecule #1: Cryo-EM structure of a bacterial protein

SupramoleculeName: Cryo-EM structure of a bacterial protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Paenibacillus sp. 453mf (bacteria)
Molecular weightTheoretical: 400 KDa

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Macromolecule #1: bacterial protein

MacromoleculeName: bacterial protein / type: protein_or_peptide / ID: 1 / Details: AMPPNP, MG / Enantiomer: LEVO
Source (natural)Organism: Paenibacillus sp. 453mf (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MIGVNRMTEA STYIGTVQDV NGANIRVVLD INTISSLKFV DGQGYRIGQI GSFVRIPIGY INLFGIVSQV GAGAVPDKLL EVEPYGHRWI SVQLVGEEGI KKEFERGVSQ YPTIGDKVHI VTEPDLKKIY GTQNKKYISL GNIASVDSIP ALVNIDTLVT RHSAVLGSTG ...String:
MIGVNRMTEA STYIGTVQDV NGANIRVVLD INTISSLKFV DGQGYRIGQI GSFVRIPIGY INLFGIVSQV GAGAVPDKLL EVEPYGHRWI SVQLVGEEGI KKEFERGVSQ YPTIGDKVHI VTEPDLKKIY GTQNKKYISL GNIASVDSIP ALVNIDTLVT RHSAVLGSTG SGKSTTVTSI LQRISDMSQF PSARIIVFDI HGEYAAAFKG KAKVYKVTPS NNELKLSIPY WALTCDEFLS VAFGGLEGSG RNALIDKIYE LKLQTLKRQE YEGINEDSLT VDTPIPFSIH KLWFDLYRAE ISTHYVQGSH SEENEALLLG EDGNPVQKGD SLKVVPPIYM PHTQAQGATK IYLSNRGKNI RKPLEGLASL LKDPRYEFLF NADDWSVNLD GKTNKDLDAL LETWVGSEES ISIFDLSGMP SSILDTLIGI LIRILYDSLF WSRNQPEGGR ERPLLVVLEE AHTYLGKDSR GIAIDGVRKI VKEGRKYGIG MMLVSQRPSE IDSTILSQCG TLFALRMNNS SDRNHVLGAV SDSFEGLMGM LPTLRTGEAI IIGESVRLPM RTIISPPPFG RRPDSLDPDV TAKWSNNRVQ GDYKEVLTLW RQKKVRSQRI VENIKRLPVV NEGEMTDMVR EMVTSSNILS IGYEADSMTL EIEFNHGLVY QYYDVPETLH TELLAAESHG KFFNSQIKNN YRFSRI

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 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: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 178699
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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