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- EMDB-35192: A cryoEM structure of the dimer of (S)-carbonyl reductase II -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-35192
TitleA cryoEM structure of the dimer of (S)-carbonyl reductase II
Map data
Sample
  • Organelle or cellular component: carbonyl reductase
KeywordsDimer / cryoEM / dynamic / OXIDOREDUCTASE
Biological speciesCandida parapsilosis (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLi YH / Wang C / Zhang RZ / Xu Y / Hunt JF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2018YFA0900302 China
CitationJournal: To Be Published
Title: A cryoEM structure of the dimer of (S)-carbonyl reductase II
Authors: Li YH / Wang C / Zhang RZ / Xu Y / Hunt JF
History
DepositionJan 24, 2023-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35192.png

Downloads & links

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Map

FileDownload / File: emd_35192.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.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-1.5529778 - 2.0754569
Average (Standard dev.)-0.00026838912 (±0.02840898)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35192_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35192_half_map_2.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 : carbonyl reductase

EntireName: carbonyl reductase
Components
  • Organelle or cellular component: carbonyl reductase

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Supramolecule #1: carbonyl reductase

SupramoleculeName: carbonyl reductase / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Candida parapsilosis (yeast)

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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: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 56.15 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.17 µm / Nominal defocus min: 1.37 µm / Nominal magnification: 105000
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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 248815
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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