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Yorodumi- PDB-9fee: Cryo-EM structure of Trypanosoma cruzi glycosomal malate dehydrogenase -
+Open data
-Basic information
Entry | Database: PDB / ID: 9fee | |||||||||
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Title | Cryo-EM structure of Trypanosoma cruzi glycosomal malate dehydrogenase | |||||||||
Components | malate dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / Tetramer / Metabolic enzyme | |||||||||
Function / homology | Function and homology information malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / carboxylic acid metabolic process / tricarboxylic acid cycle / cytoplasm Similarity search - Function | |||||||||
Biological species | Trypanosoma cruzi strain CL Brener (eukaryote) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.03 Å | |||||||||
Authors | Lipinski, O. / Sonani, R.R. / Blat, A. / Jemiola-Rzeminska, M. / Patel, S.N. / Sood, T. / Dubin, G. | |||||||||
Funding support | Poland, 2items
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Citation | Journal: To Be Published Title: Cryo-EM structure of Trypanosoma cruzi glycosomal malate dehydrogenase Authors: Lipinski, O. / Sonani, R.R. / Blat, A. / Jemiola-Rzeminska, M. / Patel, S.N. / Sood, T. / Dubin, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9fee.cif.gz | 229 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9fee.ent.gz | 184.3 KB | Display | PDB format |
PDBx/mmJSON format | 9fee.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9fee_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 9fee_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 9fee_validation.xml.gz | 39.7 KB | Display | |
Data in CIF | 9fee_validation.cif.gz | 60.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/9fee ftp://data.pdbj.org/pub/pdb/validation_reports/fe/9fee | HTTPS FTP |
-Related structure data
Related structure data | 50339MC 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: 35137.980 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi strain CL Brener (eukaryote) Gene: Tc00.1047053506503.69 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4DRD8, malate dehydrogenase |
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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: Tetrameric complex of glycosomal malate dehydrogenase / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.14 MDa / Experimental value: NO |
Source (natural) | Organism: Trypanosoma cruzi strain CL Brener (eukaryote) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: 3000 nm / Nominal defocus min: 900 nm |
Image recording | Electron dose: 42.25 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 312103 / Symmetry type: POINT | ||||||||||||||||||||||||
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