7RWY | pdb_00007rwy

Crystal structure of a Fe-bound RIDC1 variant in the presence of reductant

PDB DOI: https://doi.org/10.2210/pdb7RWY/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: 2.20 Å
R-Value Free:
0.259 (Depositor), 0.262 (DCC)
R-Value Work:
0.202 (Depositor), 0.206 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
View more details

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: 74.48 kDa
Atom Count: 5,463
Modeled Residue Count: 636
Deposited Residue Count: 636
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, B, C, D, E A, B, C, D, E, F	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth E] SDF format, chain S [auth F] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth E] MOL2 format, chain S [auth F] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth E] mmCIF format, chain S [auth F]	G [auth A] I [auth B] L [auth C] Q [auth D] R [auth E] G [auth A], I [auth B], L [auth C], Q [auth D], R [auth E], S [auth F]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth F]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain H [auth B] MOL2 format, chain P [auth D] MOL2 format, chain H [auth B] mmCIF format, chain P [auth D] mmCIF format, chain H [auth B]	H [auth B], P [auth D]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain P [auth D] Interactions & Density Focus chain H [auth B] Focus chain P [auth D]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain N [auth D] SDF format, chain K [auth C] SDF format, chain J [auth C] MOL2 format, chain O [auth D] MOL2 format, chain N [auth D] MOL2 format, chain K [auth C] MOL2 format, chain J [auth C] mmCIF format, chain O [auth D] mmCIF format, chain N [auth D] mmCIF format, chain K [auth C] mmCIF format, chain J [auth C]	J [auth C], K [auth C], N [auth D], O [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain J [auth C] Focus chain K [auth C] Focus chain N [auth D] Focus chain O [auth D] Interactions & Density Focus chain J [auth C] Focus chain K [auth C] Focus chain N [auth D] Focus chain O [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.259 (Depositor), 0.262 (DCC)
R-Value Work: 0.202 (Depositor), 0.206 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.55	α = 90
b = 82.68	β = 95.22
c = 74.14	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

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

Revision History (Full details and data files)

Version 1.0: 2022-06-29
Type: Initial release
Version 1.1: 2023-01-11
Changes: Database references
Version 1.2: 2023-10-25
Changes: Data collection, Refinement description
Version 1.3: 2024-12-25
Changes: Advisory, Derived calculations, Structure summary