8Y28 | pdb_00008y28

X-ray crystal structure of ALiS5-Streptavidine complex with 20% glycerol using a high-pressure cryocooling method

PDB DOI: https://doi.org/10.2210/pdb8Y28/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: 1.33 Å
R-Value Free:
0.185 (Depositor), 0.185 (DCC)
R-Value Work:
0.148 (Depositor), 0.147 (DCC)
R-Value Observed:
0.150 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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: 51.58 kDa
Atom Count: 4,269
Modeled Residue Count: 476
Deposited Residue Count: 484
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth D] SDF format, chain H [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth D] MOL2 format, chain H [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth D] mmCIF format, chain H [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], H [auth C], J [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain J [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain J [auth D]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain F [auth A] MOL2 format, chain I [auth C] MOL2 format, chain F [auth A] mmCIF format, chain I [auth C] mmCIF format, chain F [auth A]	F [auth A], I [auth C]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.33 Å
R-Value Free: 0.185 (Depositor), 0.185 (DCC)
R-Value Work: 0.148 (Depositor), 0.147 (DCC)
R-Value Observed: 0.150 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.666	α = 90
b = 85.553	β = 98.87
c = 58.343	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-29

Deposition Author(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

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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.