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- PDB-6wkt: Cu(I)-bound Copper Storage Protein BsCsp3 -

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Basic information

Entry
Database: PDB / ID: 6wkt
TitleCu(I)-bound Copper Storage Protein BsCsp3
ComponentsCsp3
KeywordsMETAL BINDING PROTEIN / small protein (47 kDa) / Z-contrast enhancement in cryo-EM / copper storage protein
Function / homologyProtein 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 speciesBacillus subtilis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsChen, J.Z. / Oken, A. / Dennison, C. / Lee, J. / David, S.
Funding support United States, United Kingdom, 2items
OrganizationGrant numberCountry
Other privateOHSU Startup package United States
Biotechnology and Biological Sciences Research Council (BBSRC)1668110 United Kingdom
CitationJournal: To Be Published
Title: Cu(I)-bound Copper Storage Protein BsCsp3
Authors: Chen, J.Z. / Dennison, C.
History
DepositionApr 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Csp3
B: Csp3
C: Csp3
D: Csp3


Theoretical massNumber of molelcules
Total (without water)47,4154
Polymers47,4154
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area7860 Å2
ΔGint-42 kcal/mol
Surface area16260 Å2

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Components

#1: Protein
Csp3


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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: BsCsp3, Cu(I) ions / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 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 solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMsodium chlorideNaClSodium chloride1
220 mMHEPESHEPES1
SpecimenConc.: 0.11 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse.
Specimen supportDetails: 15 mA / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: 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

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / 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 holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 95 K / Temperature (min): 90 K
Image recordingAverage 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 opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansSampling size: 15 µm / Width: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1RELION3.0-beta-2particle selection
2SerialEM3.7image acquisition
4CTFFIND4.1.5CTF correction
7PHENIX1.14-3260model fitting
9RELION3.0-beta-2initial Euler assignment
10RELION3.0-beta-2final Euler assignment
11RELION3.0-beta-2classification
12RELION3.0-beta-23D reconstruction
13PHENIX1.14-3260model refinement
Image processingDetails: The selected images were dose-weight aligned in MotionCor2 within RELION's framework
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3356122
Details: Automatic particle selections were made in RELION using a previously generated 3D reference and a low picking threshold.
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 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 buildingB value: 46.04 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 5FIG

5fig


Pdb chain-ID: A / Accession code: 5FIG / Pdb chain residue range: 4-108 / Source name: PDB / Type: experimental model

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