+Open data
-Basic information
Entry | Database: PDB / ID: 6wkt | |||||||||
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Title | Cu(I)-bound Copper Storage Protein BsCsp3 | |||||||||
Components | Csp3 | |||||||||
Keywords | METAL BINDING PROTEIN / small protein (47 kDa) / Z-contrast enhancement in cryo-EM / copper storage protein | |||||||||
Function / homology | Protein of unknown function DUF326 / Domain of Unknown Function (DUF326) / Uncharacterized cysteine-rich protein YhjQ-like / Uncharacterized cysteine-rich protein YhjQ Function and homology information | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Chen, J.Z. / Oken, A. / Dennison, C. / Lee, J. / David, S. | |||||||||
Funding support | United States, United Kingdom, 2items
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Citation | Journal: To Be Published Title: Cu(I)-bound Copper Storage Protein BsCsp3 Authors: Chen, J.Z. / Dennison, C. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6wkt.cif.gz | 76 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wkt.ent.gz | 58.8 KB | Display | PDB format |
PDBx/mmJSON format | 6wkt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/6wkt ftp://data.pdbj.org/pub/pdb/validation_reports/wk/6wkt | HTTPS FTP |
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-Related structure data
Related structure data | 21708MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 11853.758 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: yhjQ, BSU10600 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O07571 |
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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: BsCsp3, Cu(I) ions / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Value: 0.047 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Bacillus subtilis (strain 168) (bacteria) / Strain: 168 | |||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) | |||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 0.11 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse. | |||||||||||||||
Specimen support | Details: 15 mA / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 295 K Details: 5 micro-liters of sample loaded, waited 1 second,front + back blotted for 4.5 seconds at force 1 before plunging |
-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 magnification: 130000 X / Calibrated magnification: 136000 X / Nominal defocus max: 2150 nm / Nominal defocus min: 850 nm / Calibrated defocus min: 800 nm / Calibrated defocus max: 2100 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 95 K / Temperature (min): 90 K |
Image recording | Average exposure time: 0.985 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2212 Details: Images were collected at 40 frames per movie. Four movies were collected per stage shift. Frames were collected in super resolution mode at a calibrated pixel size of 0.324 A/pixel. |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Sampling size: 15 µm / Width: 5760 / Height: 4092 |
-Processing
EM software |
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Image processing | Details: The selected images were dose-weight aligned in MotionCor2 within RELION's framework | ||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3356122 Details: Automatic particle selections were made in RELION using a previously generated 3D reference and a low picking threshold. | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D2 (2x2 fold dihedral) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 121587 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 46.04 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5FIG Pdb chain-ID: A / Accession code: 5FIG / Pdb chain residue range: 4-108 / Source name: PDB / Type: experimental model |