8Y25 | pdb_00008y25

X-ray crystal structure of ALiS4-Streptavidine complex with 20% glycerol using a high-pressure cryocooling method

PDB DOI: https://doi.org/10.2210/pdb8Y25/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:
0.188 (Depositor), 0.190 (DCC)
R-Value Work:
0.139 (Depositor), 0.141 (DCC)
R-Value Observed:
0.142 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 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: 51.9 kDa
Atom Count: 4,304
Modeled Residue Count: 476
Deposited Residue Count: 484
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22629
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain M [auth D] MOL2 format, chain H [auth B] MOL2 format, chain M [auth D] mmCIF format, chain H [auth B] mmCIF format, chain M [auth D]	H [auth B], M [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain M [auth D] Interactions & Density Focus chain H [auth B] Focus chain M [auth D]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D]	E [auth A] G [auth B] I [auth C] J [auth C] K [auth C] E [auth A], G [auth B], I [auth C], J [auth C], K [auth C], L [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth D]
DMS (Subject of Investigation/LOI) Query on DMS Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]