8AQO | pdb_00008aqo

Streptavidin with a bisbiothinilated Fe4S4 cluster

PDB DOI: https://doi.org/10.2210/pdb8AQO/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Streptomyces avidinii
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-08-13 Released: 2023-08-23
Deposition Author(s): Igareta, N.V., Ward, T.R.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.217 (Depositor), 0.219 (DCC)
R-Value Work:
0.184 (Depositor), 0.192 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8AQO

Ligand Structure Quality Assessment

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

Literature

Hydrophobic probe bound to Streptavidin - 1

Igareta, N.V., Ward, T.R.

To be published.

Macromolecule Content

Total Structure Weight: 68.03 kDa
Atom Count: 4,043
Modeled Residue Count: 492
Deposited Residue Count: 632
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A, B, C, D	158	Streptomyces avidinii	Mutation(s): 2
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NUI (Subject of Investigation/LOI) Query on NUI Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain E [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth A]	E [auth A], F [auth C]	5-[(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]-~{N}-[2-[[20-[2-[5-[(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]pentanoylamino]ethanoylamino]-2$l^{3},4,12,14$l^{3},16,24,25$l^{3},27$l^{3}-octathia-1$l^{4},3$l^{4},13$l^{4},15$l^{4}-tetraferranonacyclo[11.11.1.1^{1,13}.1^{6,10}.1^{18,22}.0^{2,15}.0^{3,14}.0^{3,25}.0^{15,27}]octacosa-6(28),7,9,18,20,22(26)-hexaen-8-yl]amino]-2-oxidanylidene-ethyl]pentanamide C₄₀ H₅₂ Fe₄ N₈ O₆ S₁₀ BUAXODRGONQWCA-XTALMZNNSA-J		Interactions Focus chain E [auth A] Focus chain F [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.217 (Depositor), 0.219 (DCC)
R-Value Work: 0.184 (Depositor), 0.192 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.778	α = 90
b = 89.134	β = 97.57
c = 57.709	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-08-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-08-23
Type: Initial release
Version 1.1: 2026-03-04
Changes: Refinement description, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.