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Yorodumi- PDB-8hx1: Focused cryo-EM map of MsDps2 from MsDps2-DNA complex of Mycobact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hx1 | |||||||||
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Title | Focused cryo-EM map of MsDps2 from MsDps2-DNA complex of Mycobacterium smegmatis | |||||||||
Components | Putative starvation-induced DNA protecting protein/Ferritin and Dps | |||||||||
Keywords | DNA BINDING PROTEIN / MsDps2 / cryo-EM | |||||||||
Function / homology | Function and homology information oxidoreductase activity, acting on metal ions / ferric iron binding / DNA binding Similarity search - Function | |||||||||
Biological species | Mycolicibacterium smegmatis MC2 155 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.29 Å | |||||||||
Authors | Dutta, S. / Garg, P. | |||||||||
Funding support | India, 2items
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Citation | Journal: To Be Published Title: Focused cryo-EM map of MsDps2 from MsDps2-DNA complex of Mycobacterium smegmatis Authors: Dutta, S. / Garg, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hx1.cif.gz | 314.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hx1.ent.gz | 263.8 KB | Display | PDB format |
PDBx/mmJSON format | 8hx1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hx1_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8hx1_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8hx1_validation.xml.gz | 59.4 KB | Display | |
Data in CIF | 8hx1_validation.cif.gz | 88.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/8hx1 ftp://data.pdbj.org/pub/pdb/validation_reports/hx/8hx1 | HTTPS FTP |
-Related structure data
Related structure data | 35071MC 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: 17854.863 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria) Gene: MSMEG_3242, MSMEI_3159 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0QXB7 |
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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: Focused cryo-EM map of MsDps2 from MsDps2-DNA complex of Mycobacterium smegmatis Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2250 nm / Nominal defocus min: 750 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 171947 / Symmetry type: POINT | ||||||||||||||||||||||||
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