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- EMDB-45461: Cryo-EM structure of Candidatus Saccharibacterium phosphoketolase... -

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Basic information

Entry
Database: EMDB / ID: EMD-45461
TitleCryo-EM structure of Candidatus Saccharibacterium phosphoketolase complexed with thiamine diphosphate
Map data
Sample
  • Complex: Dimeric assembly of Candidatus Saccharibacterium phosphoketolase complexed with thiamine diphosphate
    • Protein or peptide: Phosphoketolase family protein
  • Ligand: THIAMINE DIPHOSPHATE
Keywordsacetyl-phosphate synthase / glycolaldehyde dehydration / carbohydrate metabolic process / aldehyde-lyase activity / LYASE
Function / homology
Function and homology information


aldehyde-lyase activity / carbohydrate metabolic process
Similarity search - Function
Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, C-terminal / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, N-terminal / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, thiamine diphosphate binding site / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, conserved site / D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase / XFP C-terminal domain / XFP N-terminal domain / Phosphoketolase signature 1. / Phosphoketolase signature 2. ...Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, C-terminal / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, N-terminal / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, thiamine diphosphate binding site / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, conserved site / D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase / XFP C-terminal domain / XFP N-terminal domain / Phosphoketolase signature 1. / Phosphoketolase signature 2. / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
Phosphoketolase family protein
Similarity search - Component
Biological speciesCandidatus Saccharibacteria bacterium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.18 Å
AuthorsSingal B / Landwehr G / Jewett MC
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0023278 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJun 24, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45461.png

Downloads & links

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Map

FileDownload / File: emd_45461.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 280 pix.
= 268.8 Å		0.96 Å/pix.
x 280 pix.
= 268.8 Å		0.96 Å/pix.
x 280 pix.
= 268.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0947
Minimum - Maximum-0.48504692 - 0.93313783
Average (Standard dev.)-0.0008993218 (±0.024512237)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map B

Fileemd_45461_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_45461_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dimeric assembly of Candidatus Saccharibacterium phosphoketolase ...

EntireName: Dimeric assembly of Candidatus Saccharibacterium phosphoketolase complexed with thiamine diphosphate
Components
  • Complex: Dimeric assembly of Candidatus Saccharibacterium phosphoketolase complexed with thiamine diphosphate
    • Protein or peptide: Phosphoketolase family protein
  • Ligand: THIAMINE DIPHOSPHATE

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Supramolecule #1: Dimeric assembly of Candidatus Saccharibacterium phosphoketolase ...

SupramoleculeName: Dimeric assembly of Candidatus Saccharibacterium phosphoketolase complexed with thiamine diphosphate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Candidatus Saccharibacteria bacterium phosphoketolase with mutations H58W-H132S-I479V-S523N (indexed from wild-type without a purification tag)
Source (natural)Organism: Candidatus Saccharibacteria bacterium (bacteria)
Molecular weightTheoretical: 180.40124 KDa

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Macromolecule #1: Phosphoketolase family protein

MacromoleculeName: Phosphoketolase family protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Saccharibacteria bacterium (bacteria)
Molecular weightTheoretical: 90.307164 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MWSHPQFEKG GSGNSGQNLE NIKKFIRAAN YLTVSQIFLQ DNFLLERPLT FEDIKPRLLG HWGSCPGVNW VYAHLLNIQK QLEFAKSGL KAAFMLGPGH AFPALQANLF MEETLSKVDK KATRNAQGIE YISKNFSWPG GFPSSASPFT PGVILEGGEL G YSLSTAFG ...String:
MWSHPQFEKG GSGNSGQNLE NIKKFIRAAN YLTVSQIFLQ DNFLLERPLT FEDIKPRLLG HWGSCPGVNW VYAHLLNIQK QLEFAKSGL KAAFMLGPGH AFPALQANLF MEETLSKVDK KATRNAQGIE YISKNFSWPG GFPSSASPFT PGVILEGGEL G YSLSTAFG AILDNPNLVM TTLIGDGEAE TGSIAAAWHL SKLIDPVKNG VVLPVLHLNG YKISGPTIFG SMSDFELIQF FH GAGWEPK IVDEYSAEDF DLELSNAFSN AFRDISRIKF GRNSKFIRLP MIIMRSKKGS SGVKENNGQK IEGNSLAHQV PLL KAKTDK NELEKLENWM KSYKFDELFD YERGEFKWWI NDFLPENSSR IGRNRFVDAN LNFKELKLPE ITEGFGEKSL AMNA VGSLL EKVFEKNPDN FRFFSPDETY SNKLDAIFEA TSRSWQREIK PWEKDLAKNG RVTEILSENC LQGLLQGYIL TGRYG VLTS YEAFAPVISS MMDQYAKFLA QSKEVKWRGD LASLNYILTS TGWRQDHNGF NHQNPSFIDE VLRRENGIGQ IFLPAD DNS AVAAISKMLK TRNNINVLVA GKTPEPRYFS LESAQKQLEN GGIFVFDSWK NQKITDWDSI SEDDEPDLIL AASGDYV FK ETVAALQVLL HDVAQVKIRL VYIQALCGKG IGTFENTLSK SDFVKIFTKD KPVIFAFHGY AKTLKSILFD YENPARIQ I NGYEEKGSTT TPFDMLARNK VSRYDITVRA LKSVSEGDKV FGSLVKEYRK RQDDALRFAQ ENSVDAPEIE NWDYLRFF

UniProtKB: Phosphoketolase family protein

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Macromolecule #2: THIAMINE DIPHOSPHATE

MacromoleculeName: THIAMINE DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: TPP
Molecular weightTheoretical: 425.314 Da
Chemical component information

ChemComp-TPP:
THIAMINE DIPHOSPHATE

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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

Concentration1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride
0.25 mMMgCl2magnesium chloride

Details: 50 mM HEPES, 150 mM NaCl, 0.25 mM MgCl2
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 50 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.04 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 8045 / Average exposure time: 3.1 sec. / Average electron dose: 40.0 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
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsFalcon 4i with Selectris X
Particle selectionNumber selected: 4115482 / Details: picked using Blob picker
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold predicted model
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 485609
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: Coot
Output model

PDB-9cd3:
Cryo-EM structure of Candidatus Saccharibacterium phosphoketolase complexed with thiamine diphosphate

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