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- PDB-8tjn: Crosslinked 6-deoxyerythronolide B synthase (DEBS) Module 1 in co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8tjn | |||||||||||||||
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Title | Crosslinked 6-deoxyerythronolide B synthase (DEBS) Module 1 in complex with antibody fragment 1B2: Crosslinked State 1 | |||||||||||||||
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![]() | BIOSYNTHETIC PROTEIN/IMMUNE SYSTEM / polyketide synthase / antibody / BIOSYNTHETIC PROTEIN-IMMUNE SYSTEM complex | |||||||||||||||
Function / homology | ![]() 6-deoxyerythronolide-B synthase / erythronolide synthase activity / macrolide biosynthetic process / DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.73 Å | |||||||||||||||
![]() | Cogan, D.P. / Soohoo, A.M. / Chen, M. / Brodsky, K.L. / Liu, Y. / Khosla, C. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis for Intermodular Communication in Assembly-Line Polyketide Biosynthesis Authors: Cogan, D.P. / Soohoo, A.M. / Chen, M. / Liu, Y. / Brodsky, K.L. / Khosla, C. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 523 KB | Display | ![]() |
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PDB format | ![]() | 403.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 89.8 KB | Display | |
Data in CIF | ![]() | 133.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 41305MC ![]() 8tjoC ![]() 8tjpC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 188891.219 Da / Num. of mol.: 2 Fragment: DEBS Module 1, Subunit A (UNP residues 557-2015) + EryA3 (UNP residues 2896-3172),DEBS Module 1, Subunit A (UNP residues 557-2026) + EryA3 (UNP residues 2896-3172) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q5UNP6, UniProt: Q03133, 6-deoxyerythronolide-B synthase #2: Antibody | Mass: 26447.611 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Antibody | Mass: 25715.832 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Has ligand of interest | Y | |
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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 |
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Sample preparation
Component | Name: Crosslinked DEBS Module 1 in complex with Antibody Fragment 1B2 Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES | ||||||||||||||||||||
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Molecular weight | Value: 0.48 MDa / Experimental value: YES | ||||||||||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||
Buffer solution | pH: 7.2 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 150 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 3.76 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9523 |
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Processing
EM software | Name: PHENIX / Version: 1.21_5207 / Category: model refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Particle selection | Num. of particles selected: 434136 |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84420 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT |
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |
Atomic model building | PDB-ID: 7M7F Accession code: 7M7F / Source name: PDB / Type: experimental model |
Refinement | Cross valid method: NONE |