3QVZ

Crystal structure of the Zn-RIDC1 complex stabilized by BMOE crosslinks cocrystallized in the presence of Cu(II)

• PDB DOI: https://doi.org/10.2210/pdb3QVZ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-02-26 Released: 2011-06-22 
• Deposition Author(s): Salgado, E.N., Tezcan, F.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 0.306 
• R-Value Work: 0.261 
• R-Value Observed: 0.264 

Literature

Templated construction of a zn-selective protein dimerization motif.

Salgado, E.N., Brodin, J.D., To, M.M., Tezcan, F.A.

(2011) Inorg Chem 50: 6323-6329

• PubMed: 21648390 
• DOI: https://doi.org/10.1021/ic200746m
• Primary Citation of Related Structures:  
  3QVY, 3QVZ, 3QW0, 3QW1


• PubMed Abstract: 
  

  Here, we report that the approach of metal-templated ligand synthesis can be applied to construct a dimeric protein assembly ((BMOE)RIDC1(2)), which is stabilized by noncovalent interactions and flexible covalent cross-linkers around the Zn templates. Despite its flexibility, (BMOE)RIDC1(2) selectively binds Zn(II) over other divalent metals and undergoes dimerization upon metal binding. Such simultaneous fulfillment of plasticity and selectivity is a hallmark of cellular signaling events that involve ligand/metal-induced protein dimerization.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, MC 0356, La Jolla, California 92093, USA.

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)

Macromolecule Content

• Total Structure Weight: 50.72 kDa 
• Atom Count: 3,513 
• Modelled Residue Count: 424 
• Deposited Residue Count: 424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome cb562	A, B, C, D	106	Escherichia coli	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], M [auth B], Q [auth C], W [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
ME7	F [auth A], N [auth B]	1,1'-ethane-1,2-diylbis(1H-pyrrole-2,5-dione) C10 H8 N2 O4 PUKLCKVOVCZYKF-UHFFFAOYSA-N
ZN	G [auth A], L [auth A], O [auth B], P [auth C], V [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU	H [auth A], I [auth A], J [auth A], K [auth A], R [auth C], S [auth C], T [auth C], U [auth C]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 0.306 
• R-Value Work: 0.261 
• R-Value Observed: 0.264 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.525	α = 90
b = 52.525	β = 90
c = 255.717	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-22 
Deposition Author(s): Salgado, E.N., Tezcan, F.A.

Revision History  

• Version 1.0: 2011-06-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary