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- EMDB-37569: Cryo-EM structure of a bacterial protein -

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Basic information

Entry
Database: EMDB / ID: EMD-37569
TitleCryo-EM structure of a bacterial protein
Map data
Sample
  • Complex: Cryo-EM structure of a bacterial protein
    • Protein or peptide: Helicase HerA central domain-containing protein
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Keywordsbacterial immune proteins / IMMUNE SYSTEM
Biological speciesPaenibacillus sp. 453mf (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.41 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 25, 2023-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateSep 11, 2024-
Current statusSep 11, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37569.png

Downloads & links

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Map

FileDownload / File: emd_37569.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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: 0.12
Minimum - Maximum-0.8021797 - 1.1169693
Average (Standard dev.)0.0002111255 (±0.034645095)
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_37569_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_37569_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: Helicase HerA central domain-containing protein
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

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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
Source (natural)Organism: Paenibacillus sp. 453mf (bacteria)
Molecular weightTheoretical: 400 KDa

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Macromolecule #1: Helicase HerA central domain-containing protein

MacromoleculeName: Helicase HerA central domain-containing protein / type: protein_or_peptide / ID: 1 / Details: WP_091160506.1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Paenibacillus sp. 453mf (bacteria)
Molecular weightTheoretical: 77.626344 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MIGVNRMTEA STYIGTVQDV NGANIRVVLD INTISSLKFV DGQGYRIGQI GSFVRIPIGY INLFGIVSQV GAGAVPDKLL EVEPYGHRW ISVQLVGEEG IKKEFERGVS QYPTIGDKVH IVTEPDLKKI YGTQNKKYIS LGNIASVDSI PALVNIDTLV T RHSAVLGS ...String:
MIGVNRMTEA STYIGTVQDV NGANIRVVLD INTISSLKFV DGQGYRIGQI GSFVRIPIGY INLFGIVSQV GAGAVPDKLL EVEPYGHRW ISVQLVGEEG IKKEFERGVS QYPTIGDKVH IVTEPDLKKI YGTQNKKYIS LGNIASVDSI PALVNIDTLV T RHSAVLGS TGSGKSTTVT SILQRISDMS QFPSARIIVF DIHGEYAAAF KGKAKVYKVT PSNNELKLSI PYWALTCDEF LS VAFGGLE GSGRNALIDK IYELKLQTLK RQEYEGINED SLTVDTPIPF SIHKLWFDLY RAEISTHYVQ GSHSEENEAL LLG EDGNPV QKGDSLKVVP PIYMPHTQAQ GATKIYLSNR GKNIRKPLEG LASLLKDPRY EFLFNADDWS VNLDGKTNKD LDAL LETWV GSEESISIFD LSGMPSSILD TLIGILIRIL YDSLFWSRNQ PEGGRERPLL VVLEEAHTYL GKDSRGIAID GVRKI VKEG RKYGIGMMLV SQRPSEIDST ILSQCGTLFA LRMNNSSDRN HVLGAVSDSF EGLMGMLPTL RTGEAIIIGE SVRLPM RTI ISPPPFGRRP DSLDPDVTAK WSNNRVQGDY KEVLTLWRQK KVRSQRIVEN IKRLPVVNEG EMTDMVREMV TSSNILS IG YEADSMTLEI EFNHGLVYQY YDVPETLHTE LLAAESHGKF FNSQIKNNYR FSRI

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 4 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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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: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 123238
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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