+Open data
-Basic information
Entry | Database: PDB / ID: 8hwz | |||||||||
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Title | Cryo-EM structure of delta N15 MsDps2 of Mycobacterium smegmatis | |||||||||
Components | Starvation-inducible DNA-binding protein or fine tangled pili major subunit | |||||||||
Keywords | DNA BINDING PROTEIN / Cryo-EM / N15MsDps2 | |||||||||
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: 3.56 Å | |||||||||
Authors | Garg, P. / Dutta, S. | |||||||||
Funding support | India, 2items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hwz.cif.gz | 291.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hwz.ent.gz | 241.6 KB | Display | PDB format |
PDBx/mmJSON format | 8hwz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hwz_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8hwz_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8hwz_validation.xml.gz | 58.3 KB | Display | |
Data in CIF | 8hwz_validation.cif.gz | 87.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/8hwz ftp://data.pdbj.org/pub/pdb/validation_reports/hw/8hwz | HTTPS FTP |
-Related structure data
Related structure data | 35069MC 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: 16163.995 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria) Gene: MSMEG_3242 / 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: Cryo-EM structure of delta N15 MsDps2 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 / Detector mode: COUNTING / 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 | ||||||||||||||||||||||||
Symmetry | Point symmetry: T (tetrahedral) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27741 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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