7ZXZ | pdb_00007zxz

dithiol-ligand bound to streptavidin

PDB DOI: https://doi.org/10.2210/pdb7ZXZ/pdb

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

Deposited: 2022-05-23 Released: 2022-06-15
Deposition Author(s): Igareta, N.V., Ward, T.R.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.204 (Depositor), 0.203 (DCC)
R-Value Work:
0.180 (Depositor), 0.179 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

dithiol-ligand bound to streptavidin

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

To be published.

Macromolecule Content

Total Structure Weight: 33.85 kDa
Atom Count: 2,124
Modeled Residue Count: 247
Deposited Residue Count: 316
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A, B	158	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
K9R (Subject of Investigation/LOI) Query on K9R Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B]	D [auth A], E [auth B]	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}-[(1~{R},3~{S})-3-[3,5-bis(sulfanylmethyl)phenyl]-2,4-bis(oxidanylidene)cyclopentyl]pentanamide C₂₃ H₂₉ N₃ O₄ S₃ UYYZXEJGUBQKBA-JSCGBJRHSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.204 (Depositor), 0.203 (DCC)
R-Value Work: 0.180 (Depositor), 0.179 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.324	α = 90
b = 80.79	β = 104.317
c = 46.657	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-06-15

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2022-06-15
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

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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.