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- PDB-8rj8: CytK nanopore mutant -

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Basic information

Entry
Database: PDB / ID: 8rj8
TitleCytK nanopore mutant
ComponentsCytotoxin K
KeywordsTRANSLATION / Nanopore Heptamer Transport Protein sequencing
Function / homologyBi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / cytolysis in another organism / extracellular region / Cytotoxin K
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.32 Å
AuthorsWhittaker, J.J. / Sauciuc, A. / Guskov, A.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)192.068 Netherlands
CitationJournal: To Be Published
Title: Uniformly narrow and non-sticky nanopores are required for the single-file translocation of proteins
Authors: Sauciuc, A. / Whittaker, J.J. / Tadema, M.J. / Tych, K. / Guskov, A. / Maglia, G.
History
DepositionDec 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytotoxin K
B: Cytotoxin K
C: Cytotoxin K
D: Cytotoxin K
E: Cytotoxin K
F: Cytotoxin K
G: Cytotoxin K


Theoretical massNumber of molelcules
Total (without water)239,5157
Polymers239,5157
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.229, 186.222, 104.532
Angle α, β, γ (deg.)90.00, 115.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cytotoxin K


Mass: 34216.461 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: cytK-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09KJ1
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.06 Å3/Da / Density % sol: 69.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.005 M Manganese(II) chloride tetrahydrate, 0.005 M Cobalt(II) chloride hexahydrate, 0.005 M Nickel(II) chloride hexahydrate, 0.005 M Zinc acetate dihydrate, 0.1 M MOPSO, Bis-Tris, pH 6.5, ...Details: 0.005 M Manganese(II) chloride tetrahydrate, 0.005 M Cobalt(II) chloride hexahydrate, 0.005 M Nickel(II) chloride hexahydrate, 0.005 M Zinc acetate dihydrate, 0.1 M MOPSO, Bis-Tris, pH 6.5, 35 %(w/v) glycerol, 30 %(w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 4.32→94.07 Å / Num. obs: 23236 / % possible obs: 95.69 % / Redundancy: 8 % / CC1/2: 0.9 / Net I/σ(I): 9.2
Reflection shellResolution: 4.32→4.47 Å / Num. unique obs: 1713 / CC1/2: 0.65

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.32→94.07 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 38.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.407 1261 5.51 %
Rwork0.322 --
obs-22873 95.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.32→94.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15699 0 0 0 15699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416144
X-RAY DIFFRACTIONf_angle_d0.97321971
X-RAY DIFFRACTIONf_dihedral_angle_d7.0082141
X-RAY DIFFRACTIONf_chiral_restr0.0542432
X-RAY DIFFRACTIONf_plane_restr0.0072875
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.32-4.490.2992990.23941836X-RAY DIFFRACTION73
4.49-4.690.28261320.23572505X-RAY DIFFRACTION100
4.69-4.940.31391490.24332494X-RAY DIFFRACTION100
4.94-5.250.32991480.24782514X-RAY DIFFRACTION100
5.25-5.660.32671510.25332493X-RAY DIFFRACTION100
5.66-6.220.26671190.25362547X-RAY DIFFRACTION100
6.22-7.120.37221440.31122516X-RAY DIFFRACTION100
7.13-8.980.46231860.40432472X-RAY DIFFRACTION100
8-9.40.56811330.42732235X-RAY DIFFRACTION87
Refinement TLS params.Method: refined / Origin x: -0.2489 Å / Origin y: 2.8463 Å / Origin z: 7.8079 Å
111213212223313233
T-0.2719 Å20.0895 Å20.1563 Å2--0.0178 Å2-0.0678 Å2---0.1099 Å2
L0.3638 °20.0035 °2-0.2091 °2-0.3124 °2-0.063 °2--0.1031 °2
S-0.0288 Å °0.5817 Å °-0.0793 Å °-0.4282 Å °0.1705 Å °0.0877 Å °0.0403 Å °-0.2714 Å °0.319 Å °
Refinement TLS groupSelection details: all

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