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

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Basic information

Entry
Database: PDB / ID: 8s7i
TitleFructose 6-phosphate aldolase, L107C/A129G/R134V/L163C/S166G mutant
ComponentsFructose-6-phosphate aldolase 1
KeywordsLYASE / fructose 6-phosphate aldolase / mutant / carboligation
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHebert, H. / Widersten, M.
Funding support Sweden, 1items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fructose-6-phosphate aldolase 1
B: Fructose-6-phosphate aldolase 1
C: Fructose-6-phosphate aldolase 1
D: Fructose-6-phosphate aldolase 1
E: Fructose-6-phosphate aldolase 1
F: Fructose-6-phosphate aldolase 1
G: Fructose-6-phosphate aldolase 1
H: Fructose-6-phosphate aldolase 1
I: Fructose-6-phosphate aldolase 1
J: Fructose-6-phosphate aldolase 1


Theoretical massNumber of molelcules
Total (without water)238,90710
Polymers238,90710
Non-polymers00
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Fructose-6-phosphate aldolase 1 / Fructose-6-phosphate aldolase A / FSAA


Mass: 23890.650 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Details: The TSHHHHH is a C-terminal His-tag not observed in the map
Source: (gene. exp.) Escherichia coli BL21 (bacteria) / Gene: fsaA, fsa, mipB, ybiZ, b0825, JW5109 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P78055, Lyases; Carbon-carbon lyases; Aldehyde-lyases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Fructose 6-phosphate aldolase, L107C/A129G/R134V/L163C/S166G mutant
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli BL21 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21 (bacteria) / Strain: BL21-AI
Buffer solutionpH: 8
Buffer componentConc.: 40 mM / Name: bicine / Formula: C6H13NO4
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 289 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.2 sec. / Electron dose: 50.04 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8165
Details: Images were collected in movie-mode, 40 frames with 1.251 e-/A2 dose/frame
EM imaging opticsEnergyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameCategory
1Xmippparticle selection
4CTFFINDCTF correction
7PHENIXmodel fitting
9PHENIXmodel refinement
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 307612
SymmetryPoint symmetry: D5 (2x5 fold dihedral)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115055 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 156 / Protocol: FLEXIBLE FIT / Space: REAL
Details: Initial local fitting was done using Chimera and Phenix was used for flexible fitting
Atomic model buildingPDB-ID: 3wnq

3wnq


Accession code: 3wnq / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00316370
ELECTRON MICROSCOPYf_angle_d1.01422270
ELECTRON MICROSCOPYf_dihedral_angle_d4.432340
ELECTRON MICROSCOPYf_chiral_restr0.0382700
ELECTRON MICROSCOPYf_plane_restr0.0042860

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