9XGM | pdb_00009xgm

D-alanyl carrier protein S36A

PDB DOI: https://doi.org/10.2210/pdb9XGM/pdb
Entry: 9XGM supersedes: 8I32

Classification: STRUCTURAL PROTEIN
Organism(s): Staphylococcus aureus subsp. aureus Mu50
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-10-30 Released: 2026-01-21
Deposition Author(s): Jeon, H., Lee, I.-G.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.259 (Depositor), 0.259 (DCC)
R-Value Work:
0.213 (Depositor), 0.214 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural Insights into the Staphylococcus aureus DltC-Mediated D-Alanine Transfer

Jeon, H., Lee, H., Song, C., Lee, I.G.

(2026) Biomolecules 16: 44

DOI: https://doi.org/10.3390/biom16010044

Macromolecule Content

Total Structure Weight: 18.2 kDa
Atom Count: 1,334
Modeled Residue Count: 155
Deposited Residue Count: 156
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-alanyl carrier protein	A, B	78	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 1 Gene Names: dltC, SAV0934
UniProt
Find proteins for P0A018 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore P0A018 Go to UniProtKB: P0A018
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A018
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-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: 2.10 Å
R-Value Free: 0.259 (Depositor), 0.259 (DCC)
R-Value Work: 0.213 (Depositor), 0.214 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.735	α = 90
b = 157.955	β = 90
c = 27.795	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-01-21

Deposition Author(s):

This entry supersedes: 8I32

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History (Full details and data files)

Version 1.0: 2026-01-21
Type: Initial release

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.