7PR3 | pdb_00007pr3

Cocrystal Form I of a cytochrome c, sulfonato-thiacalix[4]arene - zinc cluster

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 
    0.253 (Depositor), 0.256 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 

Literature

Protein Frameworks with Thiacalixarene and Zinc.

Flood, R.J., Ramberg, K.O., Mengel, D.B., Guagnini, F., Crowley, P.B.

(2022) Cryst Growth Des 22: 3271-3276

  • DOI: https://doi.org/10.1021/acs.cgd.2c00108
  • Primary Citation Related Structures: 
    7PR2, 7PR3, 7PR4, 7PR5

  • PubMed Abstract: 

    Controlled protein assembly provides a means to generate biomaterials. Synthetic macrocycles such as the water-soluble sulfonato-calix[n]arenes are useful mediators of protein assembly. Sulfonato-thiacalix[4]arene ( tsclx 4 ), with its metal-binding capacity, affords the potential for simultaneous macrocycle- and metal-mediated protein assembly. Here, we describe the tsclx 4 -/Zn-directed assembly of two proteins: cationic α-helical cytochrome c (cyt c ) and neutral β-propeller Ralstonia solanacearum lectin (RSL). Two co-crystal forms were obtained with cyt c , each involving multinuclear zinc sites supported by the cone conformation of tsclx 4 . The tsclx 4 /Zn cluster acted as an assembly node via both lysine encapsulation and metal-mediated protein-protein contacts. In the case of RSL, tsclx 4 adopted the 1,2-alternate conformation and supported a dinuclear zinc site with concomitant encapsulation and metal-binding of two histidine side chains. These results, together with the knowledge of thiacalixarene/metal nanoclusters, suggest promising applications for thiacalixarenes in biomaterials and MOF fabrication.

    • Organizational Affiliation: 
    • SSPC, Science Foundation Ireland Research Centre for Pharmaceuticals, School of Biological and Chemical Sciences, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland.

Macromolecule Content 

  • Total Structure Weight: 58.27 kDa 
  • Atom Count: 4,025 
  • Modeled Residue Count: 428 
  • Deposited Residue Count: 432 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c iso-1
A, B, C, D
108Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: CYC1, YJR048W, J1653
UniProt
Find proteins for P00044 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00044 
Go to UniProtKB:  P00044
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00044
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
80M
(Subject of Investigation/LOI)

Query on 80M


Download:Ideal Coordinates CCD File
BA [auth C]
G [auth A]
H [auth A]
N [auth B]
O [auth B]
BA [auth C],
G [auth A],
H [auth A],
N [auth B],
O [auth B],
RA [auth D]
sulfonato-thiacalix[4]arene
C24 H16 O16 S8
RUNCKYHXTXCYJH-UHFFFAOYSA-N
HEC

Query on HEC


Download:Ideal Coordinates CCD File
E [auth A],
L [auth B],
MA [auth D],
W [auth C]		HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
PO4

Query on PO4


Download:Ideal Coordinates CCD File
AB [auth D]
HA [auth C]
IA [auth C]
JA [auth C]
YA [auth D]
AB [auth D],
HA [auth C],
IA [auth C],
JA [auth C],
YA [auth D],
ZA [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN

Query on ZN


Download:Ideal Coordinates CCD File
AA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
F [auth A]
AA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
F [auth A],
FA [auth C],
GA [auth C],
I [auth A],
J [auth A],
K [auth A],
KA [auth D],
LA [auth D],
M [auth B],
NA [auth D],
OA [auth D],
P [auth B],
PA [auth D],
Q [auth B],
QA [auth D],
R [auth B],
S [auth B],
SA [auth D],
T [auth C],
TA [auth D],
U [auth C],
UA [auth D],
V [auth C],
VA [auth D],
WA [auth D],
X [auth C],
XA [auth D],
Y [auth C],
Z [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free:  0.253 (Depositor), 0.256 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.135α = 90
b = 79.772β = 90
c = 105.14γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Science Foundation IrelandIreland12/RC/2275_P2
Science Foundation IrelandIreland13/CDA/2168
Irish Research CouncilIrelandGOIPD/2019/513

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2022-05-18
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.3: 2025-10-01
    Changes: Advisory, Derived calculations, Structure summary