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Yorodumi- PDB-9c8s: CryoEM structure of Cryptococcus neoformans H99 Acetyl-CoA Synthe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9c8s | ||||||
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Title | CryoEM structure of Cryptococcus neoformans H99 Acetyl-CoA Synthetase in complex with adenosine-5'-ethylphosphate | ||||||
Components | Acetyl-coenzyme A synthetase | ||||||
Keywords | LIGASE / trimer | ||||||
Function / homology | Function and homology information acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process from acetate / AMP binding / mitochondrion / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Cryptococcus neoformans var. grubii H99 (fungus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.37 Å | ||||||
Authors | Xu, Z. / Schnicker, N.J. / Jezeski, A.J. / Krysan, D.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: CryoEM structure of Cryptococcus neoformans H99 Acetyl-CoA Synthetase in complex with adenosine-5'-ethylphosphate Authors: Xu, Z. / Schnicker, N.J. / Jezeski, A.J. / Krysan, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9c8s.cif.gz | 389.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9c8s.ent.gz | 249.8 KB | Display | PDB format |
PDBx/mmJSON format | 9c8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9c8s_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 9c8s_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 9c8s_validation.xml.gz | 51.4 KB | Display | |
Data in CIF | 9c8s_validation.cif.gz | 78.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/9c8s ftp://data.pdbj.org/pub/pdb/validation_reports/c8/9c8s | HTTPS FTP |
-Related structure data
Related structure data | 45309MC 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: 77475.750 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptococcus neoformans var. grubii H99 (fungus) Gene: CNAG_00797 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J9VFT1, acetate-CoA ligase #2: Chemical | 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: Cryptococcus neoformans H99 Acetyl-CoA Synthetase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 0.238 MDa / Experimental value: YES | |||||||||||||||||||||||||
Source (natural) | Organism: Cryptococcus neoformans var. grubii H99 (fungus) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 Details: 10 mM Tris pH7.5, 150 mM NaCl, 4mM MgCl2 and 10mM DTT | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 250 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 |
-Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4519578 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.2 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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