5LYC | pdb_00005lyc

Cytochrome c in complex with phosphonato-calix[6]arene

PDB DOI: https://doi.org/10.2210/pdb5LYC/pdb

Classification: OXIDOREDUCTASE
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2016-09-27 Released: 2017-05-10
Deposition Author(s): Rennie, M.L., Crowley, P.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.199 (Depositor), 0.192 (DCC)
R-Value Work:
0.169 (Depositor)
R-Value Observed:
0.170 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Protein Dimerization on a Phosphonated Calix[6]arene Disc.

Rennie, M.L., Doolan, A.M., Raston, C.L., Crowley, P.B.

(2017) Angew Chem Int Ed Engl 56: 5517-5521

PubMed: 28407337 Search on PubMed
DOI: https://doi.org/10.1002/anie.201701500
Primary Citation Related Structures:
5LYC

PubMed Abstract:
Complex formation between cationic cytochrome c and the water-soluble, poly-anionic p-phosphonatocalix[6]arene (pclx ₆ ) was investigated. A crystal structure (at 1.8 Å resolution) revealed a remarkable dimeric disc of pclx ₆ that acts like glue to mediate a symmetric (C ₂ ) protein dimer. The calixarene disc has a diameter of about 1.5 nm and masks about 360 Å ² of protein surface. The key protein-calixarene contacts occur via two linchpin lysines, with additional contacts provided by a small hydrophobic patch. The protein-calixarene supramolecular assemblies were observed in solution by size-exclusion chromatography with multi-angle light scattering and NMR spectroscopy. Using isothermal titration calorimetry and NMR data, an apparent K _d in the low micromolar range was determined for the charge-rich protein-calixarene complex. In contrast to p-sulfonatocalix[4]arene, the larger pclx ₆ has a single, well-defined binding site that mediates the assembly of cytochrome c in solution.

Organizational Affiliation

School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland.

Macromolecule Content

Total Structure Weight: 28.03 kDa
Atom Count: 2,183
Modeled Residue Count: 215
Deposited Residue Count: 216
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c iso-1	A, B	108	Saccharomyces cerevisiae S288C	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00044
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7AZ Query on 7AZ Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], H [auth B]	phosphonato-calix[6]arene C₄₂ H₄₂ O₂₄ P₆ QYHXEDFDCVRPFA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain I [auth B]	E [auth A], F [auth A], I [auth B], J [auth B], K [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.199 (Depositor), 0.192 (DCC)
R-Value Work: 0.169 (Depositor)
R-Value Observed: 0.170 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.57	α = 90
b = 54.57	β = 90
c = 208.01	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data collection
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-05-10

Deposition Author(s):

Rennie, M.L.

Crowley, P.B.

Revision History (Full details and data files)

Version 1.0: 2017-05-10
Type: Initial release
Version 2.0: 2019-09-25
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary