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- PDB-8oii: Cryo-EM KSB domain of RhiE from Burkholderia rhizoxinica -

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Basic information

Entry
Database: PDB / ID: 8oii
TitleCryo-EM KSB domain of RhiE from Burkholderia rhizoxinica
ComponentsRhiE protein,Polyketide synthase domain protein RhiE
KeywordsTRANSFERASE / Polyketide
Function / homology
Function and homology information


phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
: / : / Polyketide synthase dehydratase domain / 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 dehydratase domain / 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 / Phosphopantetheine attachment site / Thiolase-like / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsCapper, M.J. / Koehnke, J.
Funding support United Kingdom, 1items
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, M.A. / Capper, M.J. / Sundaram, S. / Fiedler, J. / Koehnke, J. / Hellmich, U. / Hertwick, C.
History
DepositionMar 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RhiE protein,Polyketide synthase domain protein RhiE
B: RhiE protein,Polyketide synthase domain protein RhiE


Theoretical massNumber of molelcules
Total (without water)231,0542
Polymers231,0542
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A3053 - 3965
2010B3053 - 3965

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Components

#1: Protein RhiE protein,Polyketide synthase domain protein RhiE / Rhizoxin synthesis polyketide synthase RhiE


Mass: 115527.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycetohabitans rhizoxinica (bacteria) / Gene: rhiE, rhiE, B0O95_10712 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A1KQS1, UniProt: I7LFI3

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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: Homodimeric complex of RhiE KSB domains / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.23 MDa / Experimental value: NO
Source (natural)Organism: Mycetohabitans rhizoxinica (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21
Buffer solutionpH: 8 / Details: 20 mM Tris-HCl pH 8
Buffer componentConc.: 20 mM / Name: Tris-HClTris
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Monodisperse sample in minimal buffer
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 288 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 120000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL
Image recordingElectron dose: 53.9 e/Å2 / Detector mode: COUNTING / Film or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Num. of grids imaged: 1 / Num. of real images: 3579
Image scansMovie frames/image: 50

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
1cryoSPARC4.2particle selection
2SerialEMimage acquisition
4CTFFIND4CTF correction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 3300635
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 393352 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
RefinementResolution: 2.84→129.92 Å / Cor.coef. Fo:Fc: 0.842 / SU B: 7.146 / SU ML: 0.131 / ESU R: 0.361
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.3682 --
obs0.3682 185005 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 74.882 Å2
Refinement stepCycle: 1 / Total: 14940
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00514380
ELECTRON MICROSCOPYf_angle_d0.49319522
ELECTRON MICROSCOPYf_dihedral_angle_d4.5181970
ELECTRON MICROSCOPYf_chiral_restr0.0422148
ELECTRON MICROSCOPYf_plane_restr0.0052558
Refine LS restraints NCS

Ens-ID: 1 / Number: 62868 / Refine-ID: ELECTRON MICROSCOPY / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.84→2.914 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork2.754 13661 -
obs--100 %

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