8BY1 | pdb_00008by1

streptavidin with an iridium catalyst for CH activation

PDB DOI: https://doi.org/10.2210/pdb8BY1/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Streptomyces avidinii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-12-11 Released: 2023-12-20
Deposition Author(s): Igareta, N.V., Ward, T.R.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free:
0.195 (Depositor), 0.203 (DCC)
R-Value Work:
0.173 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

streptavidin mutant S112I with an iridium catalyst for CH activation

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

To be published.

Macromolecule Content

Total Structure Weight: 14.11 kDa
Atom Count: 1,130
Modeled Residue Count: 123
Deposited Residue Count: 123
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A	123	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
NOF (Subject of Investigation/LOI) Query on NOF 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]	tert-butyl 7'-[5-[(3aS,4S,6aR)-2-oxidanylidene-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]-1-chloranyl-2,3,4,5,6-pentamethyl-spiro[1$l^{8}-iridapentacyclo[2.2.0.0^{1,3}.0^{1,5}.0^{2,6}]hexane-1,2'-3-aza-1-azonia-2$l^{8}-iridatricyclo[6.3.1.0^{4,12}]dodeca-1(11),4,6,8(12),9-pentaene]-3'-carboxylate C₃₄ H₄₅ Cl Ir N₅ O₄ S NIFXELQADIYDEE-HVXVAELJSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free: 0.195 (Depositor), 0.203 (DCC)
R-Value Work: 0.173 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.657	α = 90
b = 57.657	β = 90
c = 183.626	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-12-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-12-20
Type: Initial release
Version 1.1: 2023-12-27
Changes: Derived calculations

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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.