8TY0 | pdb_00008ty0

Streptavidin variant S112E-K121H bound to bis-biotinylated Iron-porphyrin

PDB DOI: https://doi.org/10.2210/pdb8TY0/pdb

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

Deposited: 2023-08-24 Released: 2024-09-11
Deposition Author(s): Follmer, A.H., Jakob, R.P., Mukherjee, M., Ward, T.R.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free:
0.191 (Depositor), 0.194 (DCC)
R-Value Work:
0.173 (Depositor), 0.176 (DCC)
R-Value Observed:
0.174 (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

Artificial Peroxidase Based on the Biotin-Streptavidin Technology that Rivals the Efficiency of Natural Peroxidases

Mukherjee, M., Waser, V., Morris, E.F., Igareta, N.V., Follmer, A.H., Jakob, R.P., Uzumcu, D., Maier, T., Ward, T.R.

(2024) ACS Catal 14: 16266-16276

DOI: https://doi.org/10.1021/acscatal.4c03208

Macromolecule Content

Total Structure Weight: 68.31 kDa
Atom Count: 4,872
Modeled Residue Count: 496
Deposited Residue Count: 632
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A, B, C, D	158	Streptomyces avidinii	Mutation(s): 0
UniProt
Find proteins for P22629 (Streptomyces avidinii) Explore P22629 Go to UniProtKB: P22629
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22629
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SIK (Subject of Investigation/LOI) Query on SIK Download Ideal Coordinates CCD File SDF format, chain E [auth C] SDF format, chain F [auth D] MOL2 format, chain E [auth C] MOL2 format, chain F [auth D] mmCIF format, chain E [auth C] mmCIF format, chain F [auth D]	E [auth C], F [auth D]	Bis-biotinylated Iron-porphyrin C₄₈ H₅₆ Fe N₁₂ O₁₂ S₄ SHOKMELSWGAVRS-NASSDBTJSA-N		Interactions Focus chain E [auth C] Focus chain F [auth D] Interactions & Density Focus chain E [auth C] Focus chain F [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.191 (Depositor), 0.194 (DCC)
R-Value Work: 0.173 (Depositor), 0.176 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 192.487	α = 90
b = 57.72	β = 107.44
c = 57.77	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-09-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	--

Revision History (Full details and data files)

Version 1.0: 2024-09-11
Type: Initial release
Version 1.1: 2025-10-01
Changes: Database references, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.