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- PDB-9xgm: D-alanyl carrier protein S36A -

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Basic information

Entry
Database: PDB / ID: 9xgm
TitleD-alanyl carrier protein S36A
ComponentsD-alanyl carrier protein
KeywordsSTRUCTURAL PROTEIN / ligase
Function / homology
Function and homology information


D-alanyl carrier activity / lipoteichoic acid biosynthetic process / cell wall organization / cytoplasm
Similarity search - Function
D-alanyl carrier protein / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
D-alanyl carrier protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJeon, H. / Lee, I.-G.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Biomolecules / Year: 2025
Title: Structural Insights into the Staphylococcus aureus DltC-Mediated D-Alanine Transfer.
Authors: Jeon, H. / Lee, H. / Song, C. / Lee, I.G.
History
DepositionOct 30, 2025Deposition site: PDBJ / Processing site: PDBJ
SupersessionJan 21, 2026ID: 8I32
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2026Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.pdbx_database_id_PubMed ..._citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-alanyl carrier protein
B: D-alanyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1983
Polymers18,1062
Non-polymers921
Water1,18966
1
B: D-alanyl carrier protein
hetero molecules

A: D-alanyl carrier protein


Theoretical massNumber of molelcules
Total (without water)18,1983
Polymers18,1062
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area1510 Å2
ΔGint-17 kcal/mol
Surface area8310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.735, 157.955, 27.795
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein D-alanyl carrier protein / DCP / D-alanine--poly(phosphoribitol) ligase subunit 2


Mass: 9053.144 Da / Num. of mol.: 2 / Mutation: S36A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Gene: dltC, SAV0934 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A018
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: PEG 8000 20.5% PEG 400 20% 100mM MgCl2 100mM pH 7.0 Tris-HCl

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.09→32.05 Å / Num. obs: 8960 / % possible obs: 99 % / Redundancy: 12.1 % / CC1/2: 0.996 / Net I/σ(I): 24.6
Reflection shellResolution: 2.09→2.17 Å / Num. unique obs: 8957 / CC1/2: 0.868

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: 000)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→32.05 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2592 896 10 %RANDOM
Rwork0.2134 ---
obs0.2179 8957 98.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→32.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1268 0 0 66 1334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011281
X-RAY DIFFRACTIONf_angle_d0.9911733
X-RAY DIFFRACTIONf_dihedral_angle_d17.265488
X-RAY DIFFRACTIONf_chiral_restr0.056203
X-RAY DIFFRACTIONf_plane_restr0.008231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.230.31831470.25731316X-RAY DIFFRACTION100
2.23-2.40.26531470.22661321X-RAY DIFFRACTION100
2.4-2.650.28291460.23861322X-RAY DIFFRACTION100
2.65-3.030.29511490.23091340X-RAY DIFFRACTION99
3.03-3.810.25481470.21051323X-RAY DIFFRACTION98
3.81-32.050.22971600.18971439X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 28.5346 Å / Origin y: 58.2237 Å / Origin z: 16.8203 Å
111213212223313233
T0.157 Å20.0435 Å2-0.0085 Å2-0.1545 Å2-0.0341 Å2--0.134 Å2
L1.4928 °20.2589 °2-0.1641 °2-1.3193 °2-0.3159 °2--1.0549 °2
S0.0248 Å °0.0134 Å °-0.1588 Å °-0.059 Å °-0.028 Å °-0.0671 Å °0.0481 Å °0.0414 Å °0.0163 Å °
Refinement TLS groupSelection details: all

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