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- EMDB-16892: Cryo-EM KSB domain of RhiE from Burkholderia rhizoxinica -

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Basic information

Entry
Database: EMDB / ID: EMD-16892
TitleCryo-EM KSB domain of RhiE from Burkholderia rhizoxinica
Map data
Sample
  • Complex: Homodimeric complex of RhiE KSB domains
    • Protein or peptide: RhiE protein,Polyketide synthase domain protein RhiE
KeywordsPolyketide / TRANSFERASE
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / fatty acid synthase activity / secondary metabolite biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
: / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily ...: / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / PKS_KR / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
RhiE protein / Polyketide synthase domain protein RhiE
Similarity search - Component
Biological speciesMycetohabitans rhizoxinica (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsCapper MJ / Koehnke J
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/W003090/1 United Kingdom
CitationJournal: To Be Published
Title: Structural Analysis of a Chain-Branching Polyketide Synthase Module
Authors: Dell M / Tran MA / Capper MJ / Sundaram S / Fiedler J / Koehnke J / Hellmich U / Hertwick C
History
DepositionMar 22, 2023-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16892.png

Downloads & links

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Map

FileDownload / File: emd_16892.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.015 Å
Density
Contour LevelBy AUTHOR: 0.178
Minimum - Maximum-0.3736496 - 0.878157
Average (Standard dev.)-0.0010179159 (±0.025903016)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 259.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16892_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_16892_additional_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_16892_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_16892_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Homodimeric complex of RhiE KSB domains

EntireName: Homodimeric complex of RhiE KSB domains
Components
  • Complex: Homodimeric complex of RhiE KSB domains
    • Protein or peptide: RhiE protein,Polyketide synthase domain protein RhiE

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Supramolecule #1: Homodimeric complex of RhiE KSB domains

SupramoleculeName: Homodimeric complex of RhiE KSB domains / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycetohabitans rhizoxinica (bacteria)
Molecular weightTheoretical: 230 KDa

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Macromolecule #1: RhiE protein,Polyketide synthase domain protein RhiE

MacromoleculeName: RhiE protein,Polyketide synthase domain protein RhiE / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycetohabitans rhizoxinica (bacteria)
Molecular weightTheoretical: 115.527039 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MKHHHHHHHH GGLVPRGSHG GSSGERVEDN ELANYIAVIG LGGYYPGADS IDELWQNLAN GVDCMSDFPA DRWDHSKIYY KNRKVLGKT TCINGSFIKD VDKFDYSYFK MPKVYADHMS PEVRLFLQVA VHTFEDAGYS KETLLSRYNG DVGVLLGTMS N DYHYYGFE ...String:
MKHHHHHHHH GGLVPRGSHG GSSGERVEDN ELANYIAVIG LGGYYPGADS IDELWQNLAN GVDCMSDFPA DRWDHSKIYY KNRKVLGKT TCINGSFIKD VDKFDYSYFK MPKVYADHMS PEVRLFLQVA VHTFEDAGYS KETLLSRYNG DVGVLLGTMS N DYHYYGFE SNVFRGSMAS GSGMATIPMT VSYFYGLTGP SLFIDTMCSS SSTCIHTACQ MLKHDETKMV LAGGLNLMYH PY TTVNTSQ GNFTSITSES VNSYGVGADG TVIGEGIGAV LLKRLDRAIA DRDQIYGVIK GSAMTNAGER NGFNVPNPDL QTL AIRQAM DQAKVHPSSI SYIEGHGSGT KLGDPIEVLG LNNAFRWATD DKQFCYLGSI KSNIGHLLAA SGIAGLTKTL LQFK HKQIA PSIHSSQLNQ DIDFADTPFV VPQQLIEWRQ PERIINGRKQ VFPRRAGLTS IAAGGMNAHM IVEEYPEPAD SAGQI SEDQ LVFVFSVHKL ALLAQNLTSF RDWLASSEAP LAQIAYTLQV GKNNLRNRLA IRCRTRQALS RALNACIDGH YQSSAD SKI FYRFQESDAV QPLESDLNDP LAPLLTQWLN GDSQVDWASL YAQPPVRISL PAYRFEKTRC WYTEEGYESS IVNPLMF KN KLHPLVAKNC STPQPGAIFR TDFVEDELLD YVYSGRGGRR LSAFNFADVA LAMPALASRF DGRTLSVSCA FEHYIADW T TVTGLEYRLF EIDSEQLELE FDFRRSGEQP THLGFAVINP LTSDEPPLPQ QWLDDARELL NRQALQAGRQ LSAAEVSQR LAQAGYDFAP YLDHDGELTI GRSGLVLKGR PPVNRHNHYA DNVQLSPYLA TTIDKALYLL LDELGLPQGR VIVRNIERLC CYHTPAGGF SVVLSGIGLN DNELSLSLLV LDEREQICVK LDKVSLYLGK QEVASVDRKH SLLTGEERMA EFKQEAKPQA D DSEAGFGE KILAFIQQEL QDKLGFAADI GESTQVHDLG LDSIMVVQLT DSVNKRFGTK LMPDLFYEKQ QLGELVARLE AA A

UniProtKB: RhiE protein, Polyketide synthase domain protein RhiE

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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

Concentration6 mg/mL
BufferpH: 8 / Component - Concentration: 20.0 mM / Component - Name: Tris-HCl / Details: 20 mM Tris-HCl pH 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK III
DetailsMonodisperse sample in minimal buffer

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3579 / Average electron dose: 53.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: JEOL / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 3300635
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 393352
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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