8IOM | pdb_00008iom

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

PDB DOI: https://doi.org/10.2210/pdb8IOM/pdb

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

Deposited: 2023-03-12 Released: 2023-04-05
Deposition Author(s): Yang, J., Hu, N.J.
Funding Organization(s): National Science Council (NSC, Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.219 (Depositor), 0.220 (DCC)
R-Value Work:
0.196 (Depositor), 0.200 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Structure of colicin Ib Channel domain at 3.0 Angstroms resolution

Yang, 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 1B	A	205	Shigella flexneri	Mutation(s): 0 Gene Names: CBL31_01480
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.219 (Depositor), 0.220 (DCC)
R-Value Work: 0.196 (Depositor), 0.200 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.994	α = 90
b = 91.994	β = 90
c = 113.896	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
HKL-2000	data scaling
PHENIX	model building

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-04-05

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Council (NSC, Taiwan)	Taiwan	110-2311-B-005-005-MY3

Revision History (Full details and data files)

Version 1.0: 2023-04-05
Type: Initial release
Version 2.0: 2023-11-15
Type: Coordinate replacement
Reason: Sequence discrepancy
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary

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.