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- EMDB-27070: apo form Cryo-EM structure of Campylobacter jejune ketol-acid red... -

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Basic information

Entry
Database: EMDB / ID: EMD-27070
Titleapo form Cryo-EM structure of Campylobacter jejune ketol-acid reductoisommerase crosslinked by Glutaraldehyde
Map dataCampylobacter jejune ketol-acid reductoisommerase crosslinked by Glutaraldehyde
Sample
  • Complex: Campylobacter jejuni ketol-acid reductoisomerase
    • Protein or peptide: Ketol-acid reductoisomerase (NADP(+))
  • Ligand: PENTANEDIAL
Keywordsketol-acid reductoisomerase / Isomerase / enzyme stability / dodecamer / branched-chain amino acid
Function / homology
Function and homology information


ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / L-valine biosynthetic process / isoleucine biosynthetic process / isomerase activity / NADP binding / magnesium ion binding / cytosol
Similarity search - Function
Ketol-acid reductoisomerase, prokaryotic / Ketol-acid reductoisomerase, C-terminal / Ketol-acid reductoisomerase / Ketol-acid reductoisomerase, N-terminal / Ketol-acid reductoisomerase, C-terminal domain / Acetohydroxy acid isomeroreductase, NADPH-binding domain / KARI N-terminal domain profile. / KARI C-terminal domain profile. / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Ketol-acid reductoisomerase (NADP(+))
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
Methodsingle particle reconstruction / Resolution: 2.94 Å
AuthorsZheng S / Guddat LW
Funding support Australia, 1 items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP210101802 Australia
CitationJournal: Appl Biosci / Year: 2022
Title: Enhancing the Thermal and Kinetic Stability of Ketol-Acid Reductoisomerase, a Central Catalyst of a Cell-Free Enzyme Cascade for the Manufacture of Platform Chemicals
Authors: Lv Y / Zheng S / Goldenzweig A / Liu F / Gao Y / Yang X / Kandale A / McGeary RP / Williams S / Kobe B / Schembri MA / Landsberg MJ / Wu B / Bruck TB / Sieber V / Boden M / Rao Z / Fleishman ...Authors: Lv Y / Zheng S / Goldenzweig A / Liu F / Gao Y / Yang X / Kandale A / McGeary RP / Williams S / Kobe B / Schembri MA / Landsberg MJ / Wu B / Bruck TB / Sieber V / Boden M / Rao Z / Fleishman SJ / Schenk G / Guddat LW
History
DepositionMay 23, 2022-
Header (metadata) releaseFeb 1, 2023-
Map releaseFeb 1, 2023-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27070.png

Downloads & links

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Map

FileDownload / File: emd_27070.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCampylobacter jejune ketol-acid reductoisommerase crosslinked by Glutaraldehyde
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 448 pix.
= 367.36 Å		0.82 Å/pix.
x 448 pix.
= 367.36 Å		0.82 Å/pix.
x 448 pix.
= 367.36 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: 0.41
Minimum - Maximum-1.9374194 - 3.6383867
Average (Standard dev.)0.00015151664 (±0.0948297)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 367.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map 1

Fileemd_27070_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_27070_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Campylobacter jejuni ketol-acid reductoisomerase

EntireName: Campylobacter jejuni ketol-acid reductoisomerase
Components
  • Complex: Campylobacter jejuni ketol-acid reductoisomerase
    • Protein or peptide: Ketol-acid reductoisomerase (NADP(+))
  • Ligand: PENTANEDIAL

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Supramolecule #1: Campylobacter jejuni ketol-acid reductoisomerase

SupramoleculeName: Campylobacter jejuni ketol-acid reductoisomerase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Campylobacter jejuni (Campylobacter)
Molecular weightTheoretical: 450 kDa/nm

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Macromolecule #1: Ketol-acid reductoisomerase (NADP(+))

MacromoleculeName: Ketol-acid reductoisomerase (NADP(+)) / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Campylobacter jejuni (Campylobacter)
Molecular weightTheoretical: 35.665953 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ITVYYDKDCD LNLIKSKKVA IIGFGSQGHA HAMNLRDNGV NVTIGLREGS VSAVKAKNAG FEVMSVSEAS KIADVIMILA PDEIQADIF NVEIKPNLSE GKAIAFAHGF NIHYGQIVVP KGVDVIMIAP KAPGHTVRNE FTLGGGTPCL IAIHQDESKN A KNLALSYA ...String:
ITVYYDKDCD LNLIKSKKVA IIGFGSQGHA HAMNLRDNGV NVTIGLREGS VSAVKAKNAG FEVMSVSEAS KIADVIMILA PDEIQADIF NVEIKPNLSE GKAIAFAHGF NIHYGQIVVP KGVDVIMIAP KAPGHTVRNE FTLGGGTPCL IAIHQDESKN A KNLALSYA SAIGGGRTGI IETTFKAETE TDLFGEQAVL CGGLSALIQA GFETLVEAGY EPEMAYFECL HEMKLIVDLI YQ GGIADMR YSISNTAEYG DYITGPKIIT EETKKAMKGV LKDIQNGVFA KDFILERRAG FARMHAERKN MNDSLIEKTG RNL RAMMPW IS

UniProtKB: Ketol-acid reductoisomerase (NADP(+))

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Macromolecule #2: PENTANEDIAL

MacromoleculeName: PENTANEDIAL / type: ligand / ID: 2 / Number of copies: 12 / Formula: PTD
Molecular weightTheoretical: 100.116 Da
Chemical component information

ChemComp-PTD:
PENTANEDIAL

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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: 1.2 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: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74899
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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