7SU2 | pdb_00007su2

Crystal structure of a Co-bound RIDC1 variant

PDB DOI: https://doi.org/10.2210/pdb7SU2/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-11-15 Released: 2022-06-29
Deposition Author(s): Golub, E., Kakkis, A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States), European Molecular Biology Organization (EMBO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.232 (Depositor), 0.234 (DCC)
R-Value Work:
0.184 (Depositor), 0.185 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Redox- and metal-directed structural diversification in designed metalloprotein assemblies.

Kakkis, A., Golub, E., Choi, T.S., Tezcan, F.A.

(2022) Chem Commun (Camb) 58: 6958-6961

PubMed: 35642584 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1039/d2cc02440c
Primary Citation Related Structures:
7RWU, 7RWV, 7RWW, 7RWX, 7RWY, 7SU2, 7TEP

PubMed Abstract:
Herein we describe a designed protein building block whose self-assembly behaviour is dually gated by the redox state of disulphide bonds and the identity of exogenous metal ions. This protein construct is shown - through extensive structural and biophysical characterization - to access five distinct oligomeric states, exemplifying how the complex interplay between hydrophobic, metal-ligand, and reversible covalent interactions could be harnessed to obtain multiple, responsive protein architectures from a single building block.

Organizational Affiliation

Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA. tezcan@ucsd.edu.

Macromolecule Content

Total Structure Weight: 49.34 kDa
Atom Count: 3,720
Modeled Residue Count: 424
Deposited Residue Count: 424
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562	A [auth D], B [auth A], C, D [auth G]	106	Escherichia coli	Mutation(s): 13 Gene Names: cybC
UniProt
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7 Go to UniProtKB: P0ABE7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0ABE7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain K [auth G] SDF format, chain I [auth C] SDF format, chain G [auth A] SDF format, chain E [auth D] MOL2 format, chain K [auth G] MOL2 format, chain I [auth C] MOL2 format, chain G [auth A] MOL2 format, chain E [auth D] mmCIF format, chain K [auth G] mmCIF format, chain I [auth C] mmCIF format, chain G [auth A] mmCIF format, chain E [auth D]	E [auth D], G [auth A], I [auth C], K [auth G]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain E [auth D] Focus chain G [auth A] Focus chain I [auth C] Focus chain K [auth G] Interactions & Density Focus chain E [auth D] Focus chain G [auth A] Focus chain I [auth C] Focus chain K [auth G]
CO (Subject of Investigation/LOI) Query on CO Download:Ideal Coordinates CCD File SDF format, chain L [auth G] SDF format, chain J [auth C] SDF format, chain H [auth A] SDF format, chain F [auth D] MOL2 format, chain L [auth G] MOL2 format, chain J [auth C] MOL2 format, chain H [auth A] MOL2 format, chain F [auth D] mmCIF format, chain L [auth G] mmCIF format, chain J [auth C] mmCIF format, chain H [auth A] mmCIF format, chain F [auth D]	F [auth D], H [auth A], J [auth C], L [auth G]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain F [auth D] Focus chain H [auth A] Focus chain J [auth C] Focus chain L [auth G] Interactions & Density Focus chain F [auth D] Focus chain H [auth A] Focus chain J [auth C] Focus chain L [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.232 (Depositor), 0.234 (DCC)
R-Value Work: 0.184 (Depositor), 0.185 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.875	α = 90
b = 90.024	β = 95.907
c = 52.042	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-06-29

Deposition Author(s):

Golub, E.

Kakkis, A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	European Union	T32GM112584
National Science Foundation (NSF, United States)	European Union	CHE1607145
European Molecular Biology Organization (EMBO)	European Union	ALTF 1336-2015