9K2H | pdb_00009k2h

Crystal structure of the carboxy-terminal channel-forming domain of Colicin Ib

PDB DOI: https://doi.org/10.2210/pdb9K2H/pdb

Classification: ANTIMICROBIAL PROTEIN
Organism(s): Shigella flexneri 2b
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-10-17 Released: 2024-11-20
Deposition Author(s): Yang, J., Hu, N.-J.
Funding Organization(s): National Science Council (NSC, Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.11 Å
R-Value Free:
0.231 (Depositor), 0.230 (DCC)
R-Value Work:
0.198 (Depositor), 0.199 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The structure of colicin Ib channel-forming domain

Yang, J., Hu, N.-J.

To be published.

Macromolecule Content

Total Structure Weight: 23.08 kDa
Atom Count: 1,529
Modeled Residue Count: 194
Deposited Residue Count: 205
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Colicin Ib protein	A	205	Shigella flexneri 2b	Mutation(s): 0 Gene Names: cib
UniProt
Find proteins for Q7DJZ6 (Shigella sonnei) Explore Q7DJZ6 Go to UniProtKB: Q7DJZ6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7DJZ6
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.11 Å
R-Value Free: 0.231 (Depositor), 0.230 (DCC)
R-Value Work: 0.198 (Depositor), 0.199 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.742	α = 90
b = 90.742	β = 90
c = 113.391	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-11-20

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Council (NSC, Taiwan)	Taiwan	113-2311-B-055-004

Revision History (Full details and data files)

Version 1.0: 2024-11-20
Type: Initial release

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.