8RJ8 | pdb_00008rj8

CytK nanopore mutant

PDB DOI: https://doi.org/10.2210/pdb8RJ8/pdb

Classification: TRANSLATION
Organism(s): Bacillus cereus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-12-20 Released: 2025-01-01
Deposition Author(s): Whittaker, J.J., Sauciuc, A., Guskov, A.
Funding Organization(s): Netherlands Organisation for Scientific Research (NWO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.32 Å
R-Value Free:
0.407 (Depositor), 0.400 (DCC)
R-Value Work:
0.322 (Depositor), 0.326 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Uniformly narrow and non-sticky nanopores are required for the single-file translocation of proteins

Sauciuc, A., Whittaker, J.J., Tadema, M.J., Tych, K., Guskov, A., Maglia, G.

To be published.

Macromolecule Content

Total Structure Weight: 239.52 kDa
Atom Count: 15,699
Modeled Residue Count: 2,012
Deposited Residue Count: 2,170
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytotoxin K	A, B, C, D, E A, B, C, D, E, F, G	310	Bacillus cereus	Mutation(s): 0 Gene Names: cytK-1
UniProt
Find proteins for Q09KJ1 (Bacillus cereus) Explore Q09KJ1 Go to UniProtKB: Q09KJ1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q09KJ1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.32 Å
R-Value Free: 0.407 (Depositor), 0.400 (DCC)
R-Value Work: 0.322 (Depositor), 0.326 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.229	α = 90
b = 186.222	β = 115.85
c = 104.532	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-01

Deposition Author(s):

Whittaker, J.J.

Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research (NWO)	Netherlands	192.068

Revision History (Full details and data files)

Version 1.0: 2025-01-01
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.