7RWV | pdb_00007rwv

Crystal structure of a metal-free RIDC1 variant

• PDB DOI: https://doi.org/10.2210/pdb7RWV/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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.252 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

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 
• 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.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 49.1 kDa 
• Atom Count: 3,651 
• Modeled Residue Count: 424 
• Deposited Residue Count: 424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562	A, B, C, D	106	Escherichia coli	Mutation(s): 13  Gene Names: cybC
UniProt
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	E [auth A], F [auth B], G [auth C], H [auth D]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.252 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.58	α = 90
b = 92.58	β = 90
c = 91.26	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-29 
Deposition Author(s): Kakkis, A., Golub, E.

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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  

• 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: 2024-11-13
  Changes: Structure summary