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Yorodumi- PDB-8tpx: Crosslinked 6-deoxyerythronolide B synthase (DEBS) Module 3 in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tpx | |||||||||||||||
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Title | Crosslinked 6-deoxyerythronolide B synthase (DEBS) Module 3 in complex with antibody fragment 1B2: trans-oriented 1B2 and ACP | |||||||||||||||
Components |
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Keywords | BIOSYNTHETIC PROTEIN / polyketide synthase / antibody | |||||||||||||||
Function / homology | Function and homology information macrolide biosynthetic process / DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / oxidoreductase activity / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Saccharopolyspora erythraea (bacteria) Homo sapiens (human) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||||||||
Authors | Cogan, D.P. / Soohoo, A.M. / Chen, M. / Brodsky, K.L. / Liu, Y. / Khosla, C. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tpx.cif.gz | 500 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tpx.ent.gz | 362 KB | Display | PDB format |
PDBx/mmJSON format | 8tpx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tpx_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8tpx_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8tpx_validation.xml.gz | 76.2 KB | Display | |
Data in CIF | 8tpx_validation.cif.gz | 112.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/8tpx ftp://data.pdbj.org/pub/pdb/validation_reports/tp/8tpx | HTTPS FTP |
-Related structure data
Related structure data | 41496MC 8tjnC 8tjoC 8tjpC 8tkoC 8tpwC 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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-Components
#1: Protein | Mass: 186489.578 Da / Num. of mol.: 3 / Fragment: DEBS Module 3,DEBS Module 3,DEBS Module 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Gene: eryAII, eryA / Plasmid: pRSG34 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BAP1 References: UniProt: Q5UNP5, 6-deoxyerythronolide-B synthase #2: Antibody | | Mass: 26447.611 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) #3: Antibody | | Mass: 25715.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) 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 |
-Sample preparation
Component | Name: Crosslinked DEBS Module 3 in complex with Antibody Fragment 1B2 Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES | ||||||||||||||||||||
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Molecular weight | Value: 0.42 MDa / Experimental value: YES | ||||||||||||||||||||
Source (natural) | Organism: Saccharopolyspora erythraea (bacteria) | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: BAP1 / Plasmid: pRSG34 | ||||||||||||||||||||
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 |
-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 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: 2.79 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: 10480 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 573745 | ||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68150 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6C9U Accession code: 6C9U / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE | ||||||||||||||||||||||||||||||
Refine LS restraints |
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