9I4R | pdb_00009i4r

N-terminal Oic streptag II in Sav E44V-S45T-V47R-D67A-K121R variant

PDB DOI: https://doi.org/10.2210/pdb9I4R/pdb

Classification: PROTEIN BINDING
Organism(s): Streptomyces avidinii, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-01-26 Released: 2025-10-29
Deposition Author(s): Wang, W., Lau, K., Pojer, F., Larabi, A.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free:
0.213 (Depositor), 0.213 (DCC)
R-Value Work:
0.176 (Depositor), 0.176 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Biotin/Steptag dual cofactor system for assymetric abiotic transformation in artificial metalloenzymes

Wang, W., Ji, X., Acin, P.G., Lau, K., Pojer, F., Ward, T.R., Hu, X.

(2025) Nat Synth

DOI: https://doi.org/10.1038/s44160-025-00940-2

Macromolecule Content

Total Structure Weight: 71.18 kDa
Atom Count: 3,994
Modeled Residue Count: 509
Deposited Residue Count: 672
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A [auth B], B [auth C], C [auth D], D [auth E]	158	Streptomyces avidinii	Mutation(s): 5
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

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Oic-P-streptagII	E [auth F], F [auth G], G [auth H], H [auth I]	10	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth E] MOL2 format, chain I [auth E] mmCIF format, chain I [auth E]	I [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth E] Interactions & Density Focus chain I [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.213 (Depositor), 0.213 (DCC)
R-Value Work: 0.176 (Depositor), 0.176 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.55	α = 90
b = 105.892	β = 106.448
c = 51.246	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing
autoPROC	data processing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-29

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-10-29
Type: Initial release

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.