8CHY

Crystal structure of an 8-repeat consensus TPR superhelix with Zinc.

PDB DOI: https://doi.org/10.2210/pdb8CHY/pdb

Classification: DE NOVO PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-02-08 Released: 2024-02-21
Deposition Author(s): Liutkus, M., Rojas, A.L., Cortajarena, A.L.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.249
R-Value Work: 0.204
R-Value Observed: 0.206

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Diverse crystalline protein scaffolds through metal-dependent polymorphism.

Liutkus, M., Sasselli, I.R., Rojas, A.L., Cortajarena, A.L.

(2024) Protein Sci 33: e4971-e4971

PubMed: 38591647 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/pro.4971
Primary Citation of Related Structures:
8BU0, 8CH0, 8CHY, 8CIG, 8CKR, 8CMQ, 8CP8, 8CQP, 8CQQ, 8OT7

PubMed Abstract:
As protein crystals are increasingly finding diverse applications as scaffolds, controlled crystal polymorphism presents a facile strategy to form crystalline assemblies with controllable porosity with minimal to no protein engineering. Polymorphs of consensus tetratricopeptide repeat proteins with varying porosity were obtained through co-crystallization with metal salts, exploiting the innate metal ion geometric requirements. A single structurally exposed negative amino acid cluster was responsible for metal coordination, despite the abundance of negatively charged residues. Density functional theory calculations showed that while most of the crystals were the most thermodynamically stable assemblies, some were kinetically trapped states. Thus, crystalline porosity diversity is achieved and controlled with metal coordination, opening a new scope in the application of proteins as biocompatible protein-metal-organic frameworks (POFs). In addition, metal-dependent polymorphic crystals allow direct comparison of metal coordination preferences.

Organizational Affiliation

Centre for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance, San Sebastian, Spain.

Macromolecule Content

Total Structure Weight: 35.43 kDa
Atom Count: 2,363
Modelled Residue Count: 272
Deposited Residue Count: 292
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Crystal structure of an 8-repeat consensus TPR superhelix with Zinc.	A	292	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain S [auth A] MOL2 format, chain S [auth A]	S [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain S [auth A] Interactions & Density Focus chain S [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain M [auth A] SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain N [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain R [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain O [auth A] MOL2 format, chain R [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A]	O [auth A], P [auth A], Q [auth A], R [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain T [auth A] MOL2 format, chain T [auth A]	T [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain T [auth A] Interactions & Density Focus chain T [auth A]