9XIK | pdb_00009xik

Crystal structure of Streptavidin-2 (Sav2) complexed with acidomycin from Streptomyces avidinii

PDB DOI: https://doi.org/10.2210/pdb9XIK/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Streptomyces avidinii
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2025-11-03 Released: 2026-11-11
Deposition Author(s): Fu, C., Wu, D., Mo, J., Diao, X., Wang, T.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.204 (Depositor), 0.205 (DCC)
R-Value Work:
0.181 (Depositor), 0.184 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Multi-functional streptavidins orchestrate a synergistic network of biotin-pathway antibiotics from Streptomyces

Fu, C., Wu, D., Mo, J., Diao, X., Wang, T.

To be published.

Macromolecule Content

Total Structure Weight: 14.09 kDa
Atom Count: 1,066
Modeled Residue Count: 121
Deposited Residue Count: 129
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin-2	A	129	Streptomyces avidinii	Mutation(s): 0 Gene Names: J2Z77_006442
UniProt
Find proteins for A0ABS4LEQ1 (Streptomyces avidinii) Explore A0ABS4LEQ1 Go to UniProtKB: A0ABS4LEQ1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ABS4LEQ1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EZ5 (Subject of Investigation/LOI) Query on A1EZ5 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	6-[(2~{S})-4-oxidanylidene-1,3-thiazolidin-2-yl]hexanoic acid C₉ H₁₅ N O₃ S CSOJYIADHHNGRM-QMMMGPOBSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.204 (Depositor), 0.205 (DCC)
R-Value Work: 0.181 (Depositor), 0.184 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.861	α = 90
b = 57.861	β = 90
c = 184.202	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHENIX	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-11-11

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2026-11-11
Type: Initial release