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- EMDB-41304: Periplasmic map -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-41304
TitlePeriplasmic map
Map dataPeriplasmic map
Sample
  • Complex: RodA-PBP2
KeywordsPeptidoglycan / glycosyltransferase / enzyme / MEMBRANE PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsNygaard R / Mancia F
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM132120 United States
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis of peptidoglycan synthesis by E. coli RodA-PBP2 complex
Authors: Nygaard R / Graham CLB / Belcher Dufrisne M / Colburn JD / Pepe J / Hydorn MA / Corradi S / Brown CM / Ashraf KU / Vickery ON / Briggs NS / Deering JJ / Kloss B / Botta B / Clarke OB / ...Authors: Nygaard R / Graham CLB / Belcher Dufrisne M / Colburn JD / Pepe J / Hydorn MA / Corradi S / Brown CM / Ashraf KU / Vickery ON / Briggs NS / Deering JJ / Kloss B / Botta B / Clarke OB / Columbus L / Dworkin J / Stansfeld PJ / Roper DI / Mancia F
History
DepositionJul 21, 2023-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41304.png

Downloads & links

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Map

FileDownload / File: emd_41304.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPeriplasmic map
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.29018566 - 0.54822797
Average (Standard dev.)-0.00016388434 (±0.006868241)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 332.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map 1

Fileemd_41304_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_41304_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RodA-PBP2

EntireName: RodA-PBP2
Components
  • Complex: RodA-PBP2

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Supramolecule #1: RodA-PBP2

SupramoleculeName: RodA-PBP2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: Nanodisc were formed using MSP1E3D1 and POPG lipid
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 111.803 KDa

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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

Concentration0.66 mg/mL
BufferpH: 7
Component:
ConcentrationNameFormula
20.0 mMHEPES
150.0 mMSodium ChlorideNaClSodium chloride
1.0 mMTCEPtris(2-carboxyethyl)phosphine
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 11120 / Average exposure time: 2.5 sec. / Average electron dose: 58.5 e/Å2

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Image processing

Particle selectionNumber selected: 4415933
Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.12 and 3.2) / Software - details: Local refinement / Number images used: 104553

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Atomic model buiding 1

Initial modelPDB ID:

4f0a


Chain - Source name: PDB / Chain - Initial model type: experimental model

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