7RWU

Crystal structure of Ni-bound RIDC1 variant in the presence of reductant

PDB DOI: https://doi.org/10.2210/pdb7RWU/pdb

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

Deposited: 2021-08-20 Released: 2022-06-29
Deposition Author(s): Kakkis, A., Golub, E.
Funding Organization(s): European Molecular Biology Organization (EMBO), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.189
R-Value Work: 0.164
R-Value Observed: 0.165

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 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 PubMedSearch on PubMed Central
DOI: https://doi.org/10.1039/d2cc02440c
Primary Citation of 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: 12.61 kDa
Atom Count: 1,086
Modelled Residue Count: 106
Deposited Residue Count: 106
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562	A	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0ABE7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
NI (Subject of Investigation/LOI) Query on NI Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.189
R-Value Work: 0.164
R-Value Observed: 0.165
Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.26	α = 90
b = 94.26	β = 90
c = 94.26	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2022-06-29

Deposition Author(s):

Kakkis, A.

Golub, E.

Funding Organization	Location	Grant Number
European Molecular Biology Organization (EMBO)	United States	ALTF 1336-2015
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32GM112584
National Science Foundation (NSF, United States)	United States	CHE-1607145