8QQ3 | pdb_00008qq3

Streptavidin with a Ni-cofactor

PDB DOI: https://doi.org/10.2210/pdb8QQ3/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Streptomyces avidinii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-10-03 Released: 2024-02-07
Deposition Author(s): Zhang, K., Jakob, R.P., Ward, T.R.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.191 (Depositor), 0.204 (DCC)
R-Value Work:
0.162 (Depositor), 0.175 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

An artificial nickel chlorinase based on the biotin-streptavidin technology.

Yu, K., Zhang, K., Jakob, R.P., Maier, T., Ward, T.R.

(2024) Chem Commun (Camb) 60: 1944-1947

PubMed: 38277163 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1039/d3cc05847f
Primary Citation Related Structures:
8QQ3

PubMed Abstract:
Herein, we report on an artificial nickel chlorinase (ANCase) resulting from anchoring a biotinylated nickel-based cofactor within streptavidin (Sav). The resulting ANCase was efficient for the chlorination of diverse C(sp ³)-H bonds. Guided by the X-ray analysis of the ANCase, the activity of the artificial chlorinase could be significantly improved. This approach opens interesting perspectives for late-stage functionalization of organic intermediates as it complements biocatalytic chlorination strategies.

Organizational Affiliation

Department of Chemistry, University of Basel, Mattenstrasse 22, Basel, CH-4058, Switzerland. thomas.ward@unibas.ch.

Macromolecule Content

Total Structure Weight: 69 kDa
Atom Count: 4,400
Modeled Residue Count: 502
Deposited Residue Count: 636
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A, B, C, D	159	Streptomyces avidinii	Mutation(s): 0
UniProt
Find proteins for P22629 (Streptomyces avidinii) Explore P22629 Go to UniProtKB: P22629
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22629
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WKF (Subject of Investigation/LOI) Query on WKF Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	4-[4-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]butylamino]-~{N}1,~{N}1'-di(quinolin-8-yl)cyclohexane-1,1-dicarboxamide C₃₅ H₃₉ N₇ O₃ S RCUCAUCKUVJHRT-QYDYLWNGSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C]