9I2I | pdb_00009i2i

X-ray structure of the B1 domain of streptococcal protein G triple mutant T2Q, N8D, and N37D (GB1-QDD).

PDB DOI: https://doi.org/10.2210/pdb9I2I/pdb

Classification: IMMUNE SYSTEM
Organism(s): Streptococcus sp.
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-01-20 Released: 2025-09-03
Deposition Author(s): Engilberge, S., Becker, L.M., Kapitonova, A., Schanda, P.
Funding Organization(s): Austrian Science Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.08 Å
R-Value Free:
0.210 (Depositor), 0.209 (DCC)
R-Value Work:
0.180 (Depositor), 0.180 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes

Becker, L.M., Fu, H., Tatman, B.P., Dreydoppel, M., Kapitonova, A., Weininger, U., Engilberge, S., Chipot, C., Schanda, P.

(2025) bioRxiv

DOI: https://doi.org/10.1101/2025.08.20.671406

Macromolecule Content

Total Structure Weight: 12.48 kDa
Atom Count: 1,050
Modeled Residue Count: 110
Deposited Residue Count: 112
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin G-binding protein G	A, B	56	Streptococcus sp.	Mutation(s): 3 Gene Names: spg
UniProt
Find proteins for P19909 (Streptococcus sp. group G) Explore P19909 Go to UniProtKB: P19909
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19909
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.08 Å
R-Value Free: 0.210 (Depositor), 0.209 (DCC)
R-Value Work: 0.180 (Depositor), 0.180 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.48	α = 90
b = 35.186	β = 122.512
c = 49.943	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	--

Revision History (Full details and data files)

Version 1.0: 2025-09-03
Type: Initial release
Version 1.1: 2025-10-22
Changes: Data collection

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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.