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- EMDB-79672: Cryo-EM structure of glutamate mutase from Carboxydothermus hydro... -

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Basic information

Entry
Database: EMDB / ID: EMD-79672
TitleCryo-EM structure of glutamate mutase from Carboxydothermus hydrogenoformans in the pre-activation state
Map data
Sample
  • Complex: glutamate mutase
Keywordsglutamate mutase / adenosylcobalamin / intact Co-C bond / pre-activation state / cryo-EM / ISOMERASE
Biological speciesCarboxydothermus hydrogenoformans Z-2901 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhang XY / Tjia-Fleck SK / Tian SL
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R35GM155016 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of glutamate mutase from Carboxydothermus hydrogenoformans in the pre-activation state
Authors: Zhang XY / Tjia-Fleck SK / Tian SL
History
DepositionOct 20, 2026-
Header (metadata) releaseOct 28, 2026-
Map releaseOct 28, 2026-
UpdateOct 28, 2026-
Current statusOct 28, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_79672.png

Downloads & links

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Map

FileDownload / File: emd_79672.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 200 pix.
= 211.6 Å		1.06 Å/pix.
x 200 pix.
= 211.6 Å		1.06 Å/pix.
x 200 pix.
= 211.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.189
Minimum - Maximum-2.2880125 - 3.3998764
Average (Standard dev.)0.001010297 (±0.060635906)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 211.59999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_79672_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_79672_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 : glutamate mutase

EntireName: glutamate mutase
Components
  • Complex: glutamate mutase

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Supramolecule #1: glutamate mutase

SupramoleculeName: glutamate mutase / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Carboxydothermus hydrogenoformans Z-2901 (bacteria)

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 509882
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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