8Y27 | pdb_00008y27

X-ray crystal structure of ALiS5-Streptavidine complex with 10% glycerol using a high-pressure cryocooling method

PDB DOI: https://doi.org/10.2210/pdb8Y27/pdb

Classification: CYTOSOLIC PROTEIN
Organism(s): Streptomyces avidinii
Mutation(s): No

Deposited: 2024-01-25 Released: 2025-01-29
Deposition Author(s): Higashiura, A., Yamamoto, A., Sugiyama, S.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.185 (Depositor), 0.189 (DCC)
R-Value Work:
0.139 (Depositor), 0.154 (DCC)
R-Value Observed:
0.141 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Binding competition between substrates and cryoprotectants in protein crystals directly observed by a hybrid method of in-gel crystallization and high-pressure cryo-cooling in X-ray crystallography

Higashiura, A., Sugiyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 52.4 kDa
Atom Count: 4,412
Modeled Residue Count: 477
Deposited Residue Count: 484
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A, B, C, D	121	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1LXQ (Subject of Investigation/LOI) Query on A1LXQ Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain K [auth D] SDF format, chain H [auth C] MOL2 format, chain G [auth B] MOL2 format, chain K [auth D] MOL2 format, chain H [auth C] mmCIF format, chain G [auth B] mmCIF format, chain K [auth D] mmCIF format, chain H [auth C]	G [auth B], H [auth C], K [auth D]	dimethyl 5-(4-oxidanylidene-5~{H}-furo[3,2-c]pyridin-2-yl)benzene-1,3-dicarboxylate C₁₇ H₁₃ N O₆ RYAJKWVOTXPFPC-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth C] Focus chain K [auth D] Interactions & Density Focus chain G [auth B] Focus chain H [auth C] Focus chain K [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain F [auth A] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain F [auth A] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C] mmCIF format, chain F [auth A]	F [auth A], I [auth C], J [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth C] Focus chain J [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth C] Focus chain J [auth C]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.185 (Depositor), 0.189 (DCC)
R-Value Work: 0.139 (Depositor), 0.154 (DCC)
R-Value Observed: 0.141 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.988	α = 90
b = 85.539	β = 98.92
c = 58.367	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-29

Deposition Author(s):

Higashiura, A.

Yamamoto, A.

Sugiyama, S.

Funding Organization	Location	Grant Number
Other private	Japan	--

Revision History (Full details and data files)

Version 1.0: 2025-01-29
Type: Initial release
Version 2.0: 2025-12-24
Type: Coordinate replacement
Reason: Ligand geometry
Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary