SAXSdb — 9xgm

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1. Protein Identity and Related Structures Protein Identity & Related Structures

D-alanyl carrier protein

Staphylococcus aureus subsp. aureus Mu50

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–78 Chain B； UniProt 1–78	Mutation：S36A	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；289 K；PEG 8000 20.5% PEG 400 20% 100mM MgCl2 100mM pH 7.0 Tris-HCl	Resolution 2.10 Å R-free 0.259

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9XGM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9XGL D-alanyl carrier protein Deposited 2025-10-30	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–78（78 aa） Chain B 1–78（78 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；PEG 400, Magnesium chloride, pH 7.5 HEPES, Sodium Thiocyanate	Resolution 2.28 Å R-free 0.255
9XGL D-alanyl carrier protein Deposited 2025-10-30	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–78（78 aa） Chain D 1–78（78 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；PEG 400, Magnesium chloride, pH 7.5 HEPES, Sodium Thiocyanate	Resolution 2.28 Å R-free 0.255

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DLTC_STAAM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–78； UniProt 1–78 Author chain B； PDBConstruct 1–78； UniProt 1–78

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9xgm
Deposition date deposition_date	2025-10-30
Structure title title	D-alanyl carrier protein S36A
Keywords keywords	ligase, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	19.00 Å
Radius of gyration Rg (electron density) rg_electron	18.01 Å
Forward intensity I(0) i0	5931250.00
Molecular weight molecular_weight	17991.0 kDa
Excluded volume excluded_volume	22615 Å³
Envelope volume envelope_volume	26826 Å³
Hydration-shell volume shell_volume	13378 Å³
Envelope diameter envelope_diameter	63.0 Å
Shell Rg shell_rg	22.88 Å
Envelope Rg envelope_rg	18.26 Å
Shape Rg shape_rg	17.97 Å
Total Rg total_rg	18.95 Å
Total atoms total_atoms	2507
Residues n_residues	155
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	64.4 Å
Rg (real space) rg_real	19.10 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	5.9310e+06
I(0) uncertainty (real space) i0_real_error	7.8800e+04
Rg (reciprocal space) rg_reciprocal	19.09 Å
I(0) (reciprocal space) i0_reciprocal	5931000.0000
Solution quality estimate total_estimate	0.8372
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.8 Å
Skewness Skewness skewness	0.472
Kurtosis Kurtosis kurtosis	-0.345
Angular range angular_range	— – 0.4200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2901000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.666; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.889; Smooth: 0.991

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	D-alanyl carrier protein
Molecular weight formula_weight	9053.1 kDa
Mutation mutation	S36A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2573

MEFREQVLNLLAEVAENDIVKENPDVEIFEEGIIDAFQTVGLLLEIQNKLDIEVSIMDFDRDEWATPNKIVEALEELR

来源 Source

来源生物 organism	Staphylococcus aureus subsp. aureus Mu50
NCBI Class编号 ncbi_taxonomy_id	158878
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	66

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8. Citations (1)

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Unit-cell length a length_a	32.735 Å
Unit-cell length b length_b	157.955 Å
Unit-cell length c length_c	27.795 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	32.050 Å
R factor r_factor	0.2179
R_work r_work	0.2134
R_free r_free	0.2592

fit	/app/data/saxs_computation/xg/9xgm/9xgm.fit
pddf	/app/data/pr_computation/xg/9xgm/9xgm.pr.out
profile	/app/data/saxs_computation/xg/9xgm/9xgm.dat

D-alanyl carrier protein S36A

1. Protein Identity and Related Structures Protein Identity & Related Structures

D-alanyl carrier protein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction