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Yorodumi- EMDB-35069: Cryo-EM structure of delta N15 MsDps2 of Mycobacterium smegmatis -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35069 | |||||||||
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Title | Cryo-EM structure of delta N15 MsDps2 of Mycobacterium smegmatis | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Cryo-EM / N15MsDps2 / DNA BINDING PROTEIN | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 3.56 Å | |||||||||
Authors | Garg P / Dutta S | |||||||||
Funding support | India, 2 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of delta N15 MsDps2 of Mycobacterium smegmatis Authors: Garg P / Dutta S | |||||||||
History |
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-Structure visualization
-Downloads & links
-EMDB archive
Map data | EMDB map data format | |||
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Header (meta data) | EMDB header | |||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35069 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35069 | HTTPS FTP |
-Validation report
Summary document | emd_35069_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_35069_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_35069_validation.xml.gz | 16 KB | Display | |
Data in CIF | emd_35069_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35069 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35069 | HTTPS FTP |
-Related structure data
Related structure data | 8hwzMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_35069.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.92 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Cryo-EM structure of delta N15 MsDps2 of Mycobacterium smegmatis
Entire | Name: Cryo-EM structure of delta N15 MsDps2 of Mycobacterium smegmatis |
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Components |
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-Supramolecule #1: Cryo-EM structure of delta N15 MsDps2 of Mycobacterium smegmatis
Supramolecule | Name: Cryo-EM structure of delta N15 MsDps2 of Mycobacterium smegmatis type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
-Macromolecule #1: Starvation-inducible DNA-binding protein or fine tangled pili maj...
Macromolecule | Name: Starvation-inducible DNA-binding protein or fine tangled pili major subunit type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
Molecular weight | Theoretical: 16.163995 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: TPEFGGNLQK VLVDLIELSL QGKQAHWNVV GSNFRDLHLQ LDELVDFARE GSDTIAERMR ALDAVPDGRS DTVAATTTLP EFPAFERST ADVVDLITTR INATVDTIRR VHDAVDAEDP STADLLHGLI DGLEKQAWLI RSENRKV UniProtKB: Starvation-inducible DNA-binding protein or fine tangled pili major subunit |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.75 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Applied symmetry - Point group: T (tetrahedral) / Resolution.type: BY AUTHOR / Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 27741 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-8hwz: |