3QVY

Crystal structure of the Zn-RIDC1 complex stabilized by BMOE crosslinks

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.245 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


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

  • 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.

    • Organizational Affiliation: 

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


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome cb562
A, B, C, D
106Escherichia coliMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM
Download Ideal Coordinates CCD File 
E [auth A],
K [auth B],
Q [auth C],
V [auth D]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
ME7
Query on ME7
Download Ideal Coordinates CCD File 
O [auth C],
U [auth D]		1,1'-ethane-1,2-diylbis(1H-pyrrole-2,5-dione)
C10 H8 N2 O4
PUKLCKVOVCZYKF-UHFFFAOYSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
L [auth B],
M [auth B],
N [auth B],
P [auth C],
R [auth C],
S [auth C],
T [auth D],
W [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.245 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.088α = 90
b = 52.088β = 90
c = 253.943γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
MOSFLMdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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