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- EMDB-19773: Fructose 6-phosphate aldolase, L107C/A129G/R134V/L163C/S166G mutant -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-19773
TitleFructose 6-phosphate aldolase, L107C/A129G/R134V/L163C/S166G mutant
Map dataFructose 6-phosphate aldolase, V134G129G166C107C163 mutant
Sample
  • Complex: Fructose 6-phosphate aldolase, L107C/A129G/R134V/L163C/S166G mutant
    • Protein or peptide: Fructose-6-phosphate aldolase 1
  • Ligand: water
Keywordsfructose 6-phosphate aldolase / mutant / carboligation / LYASE
Function / homology
Function and homology information


ketone catabolic process / fructose 6-phosphate aldolase activity / Lyases; Carbon-carbon lyases; Aldehyde-lyases / fructose metabolic process / identical protein binding / cytoplasm
Similarity search - Function
Fructose-6-phosphate aldolase / Transaldolase type 3B/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase, archaeal/bacterial / Transaldolase active site. / Transaldolase, active site / Transaldolase signature 1. / Transaldolase/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase / Aldolase-type TIM barrel
Similarity search - Domain/homology
Fructose-6-phosphate aldolase 1
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHebert H / Widersten M
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Other private218-0061 Sweden
CitationJournal: To Be Published
Title: The Structure of an Engineered Aldolase Catalyzing Carboligation of Arylated Ketones and Aldehydes, Capturing the Iminium Reaction Intermediate, Points Towards a Conserved Tyrosine Residue as Catalytic Acid/Base
Authors: Hebert H / Widersten M
History
DepositionMar 1, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19773.png

Downloads & links

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Map

FileDownload / File: emd_19773.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFructose 6-phosphate aldolase, V134G129G166C107C163 mutant
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 180 pix.
= 147.6 Å		0.82 Å/pix.
x 180 pix.
= 147.6 Å		0.82 Å/pix.
x 180 pix.
= 147.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.08513269 - 0.15205924
Average (Standard dev.)0.0008227345 (±0.009987121)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 147.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Fructose 6-phosphate aldolase, V134G129G166C107C163 mutant, half1

Fileemd_19773_half_map_1.map
AnnotationFructose 6-phosphate aldolase, V134G129G166C107C163 mutant, half1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Fructose 6-phosphate aldolase, V134G129G166C107C163 mutant, half2

Fileemd_19773_half_map_2.map
AnnotationFructose 6-phosphate aldolase, V134G129G166C107C163 mutant, half2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Fructose 6-phosphate aldolase, L107C/A129G/R134V/L163C/S166G mutant

EntireName: Fructose 6-phosphate aldolase, L107C/A129G/R134V/L163C/S166G mutant
Components
  • Complex: Fructose 6-phosphate aldolase, L107C/A129G/R134V/L163C/S166G mutant
    • Protein or peptide: Fructose-6-phosphate aldolase 1
  • Ligand: water

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Supramolecule #1: Fructose 6-phosphate aldolase, L107C/A129G/R134V/L163C/S166G mutant

SupramoleculeName: Fructose 6-phosphate aldolase, L107C/A129G/R134V/L163C/S166G mutant
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli BL21 (bacteria)

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Macromolecule #1: Fructose-6-phosphate aldolase 1

MacromoleculeName: Fructose-6-phosphate aldolase 1 / type: protein_or_peptide / ID: 1
Details: The TSHHHHH is a C-terminal His-tag not observed in the map
Number of copies: 10 / Enantiomer: LEVO / EC number: Lyases; Carbon-carbon lyases; Aldehyde-lyases
Source (natural)Organism: Escherichia coli BL21 (bacteria)
Molecular weightTheoretical: 23.89065 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MELYLDTSDV VAVKALSRIF PLAGVTTNPS IIAAGKKPLD VVLPQLHEAM GGQGRLFAQV MATTAEGMVN DALKLRSIIA DIVV(A1H5N)VPVT AEGLAAIKML KAEGIPTCGT AVYGAAQGLL SALAGAEYVG PYVNVIDAQG GSGIQTVTDL HQLLK MHAP ...String:
MELYLDTSDV VAVKALSRIF PLAGVTTNPS IIAAGKKPLD VVLPQLHEAM GGQGRLFAQV MATTAEGMVN DALKLRSIIA DIVV(A1H5N)VPVT AEGLAAIKML KAEGIPTCGT AVYGAAQGLL SALAGAEYVG PYVNVIDAQG GSGIQTVTDL HQLLK MHAP QAKVCAAGFK TPRQALDCLL AGCESITLPL DVAQQMISYP AVDAAVAKFE QDWQGAFGRT SITSHHHHH

UniProtKB: Fructose-6-phosphate aldolase 1

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 272 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration2.0 mg/mL
BufferpH: 8 / Component - Concentration: 40.0 mM / Component - Formula: C6H13NO4 / Component - Name: bicine
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 8165 / Average exposure time: 2.2 sec. / Average electron dose: 50.04 e/Å2
Details: Images were collected in movie-mode, 40 frames with 1.251 e-/A2 dose/frame
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 307612
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D5 (2x5 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 115055
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final 3D classificationNumber classes: 3 / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3wnq


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsInitial local fitting was done using Chimera and Phenix was used for flexible fitting
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 156
Output model

PDB-8s7i:
Fructose 6-phosphate aldolase, L107C/A129G/R134V/L163C/S166G mutant

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