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Yorodumi- PDB-7zma: Ketosynthase domain of module 4 from Brevibacillus Brevis orphan BGC11 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zma | ||||||
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Title | Ketosynthase domain of module 4 from Brevibacillus Brevis orphan BGC11 | ||||||
Components | Putative polyketide synthase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Ketosynthase / polyketide synthase / thiolase fold / Claisen Condensation | ||||||
Function / homology | Function and homology information DIM/DIP cell wall layer assembly / secondary metabolite biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Brevibacillus brevis NBRC 100599 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
Authors | Tittes, Y.U. / Herbst, D.A. / Jakob, R.P. / Maier, T. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Sci Adv / Year: 2022 Title: The structure of a polyketide synthase bimodule core. Authors: Yves U Tittes / Dominik A Herbst / Solène F X Martin / Hugo Munoz-Hernandez / Roman P Jakob / Timm Maier / Abstract: Polyketide synthases (PKSs) are predominantly microbial biosynthetic enzymes. They assemble highly potent bioactive natural products from simple carboxylic acid precursors. The most versatile ...Polyketide synthases (PKSs) are predominantly microbial biosynthetic enzymes. They assemble highly potent bioactive natural products from simple carboxylic acid precursors. The most versatile families of PKSs are organized as assembly lines of functional modules. Each module performs one round of precursor extension and optional modification, followed by directed transfer of the intermediate to the next module. While enzymatic domains and even modules of PKSs are well understood, the higher-order modular architecture of PKS assembly lines remains elusive. Here, we visualize a PKS bimodule core using cryo-electron microscopy and resolve a two-dimensional meshwork of the bimodule core formed by homotypic interactions between modules. The sheet-like organization provides the framework for efficient substrate transfer and for sequestration of trans-acting enzymes required for polyketide production. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zma.cif.gz | 444.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zma.ent.gz | 333.9 KB | Display | PDB format |
PDBx/mmJSON format | 7zma.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zma_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7zma_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7zma_validation.xml.gz | 43.5 KB | Display | |
Data in CIF | 7zma_validation.cif.gz | 63.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/7zma ftp://data.pdbj.org/pub/pdb/validation_reports/zm/7zma | HTTPS FTP |
-Related structure data
Related structure data | 14793MC 7zm9C 7zmcC 7zmdC 7zmfC 7zskC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 187424.781 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brevibacillus brevis NBRC 100599 (bacteria) Strain: 47 / JCM 6285 / NBRC 100599 / Gene: BBR47_39880 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: C0ZGQ6 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Ketosynthase domain 4 of Brevibacillus Brevis BGC 11 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.16 MDa / Experimental value: NO |
Source (natural) | Organism: Brevibacillus brevis NBRC 100599 (bacteria) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) / Strain: SF21 |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.18 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: LEICA PLUNGER / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 293 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 67 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 171149 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.9 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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Refine LS restraints NCS | Type: NCS constraints / Rms dev position: 0.00070270488849 Å |