SAXSdb — 10pa

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

Serine-aspartate repeat-containing protein D

Staphylococcus aureus subsp. aureus JH1

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 244–561	Fragment：A2-A3 domains	EDO 1,2-ETHANEDIOL × 3 CA CALCIUM ION × 5 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；296 K；0.2 M calcium chloride and 20% (w/v) PEG 3350	Resolution 1.92 Å R-free 0.245

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 10PA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
10PS Crystal structure of SdrD A2-A3-B1-B2 domains from Staphylococcus aureus JH1 Deposited 2026-01-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 244–798（555 aa） Fragment：A2-A3-B1-B2 domains	Not recorded	CA CALCIUM ION × 9 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 7 ACT ACETATE ION × 1 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；0.1 M Tris-HCl and 20% (w/v) PEG 2000 MME	Resolution 2.00 Å R-free 0.235
8VDK Crystal Structure of LPXTG-motif Cell Wall Anchor Domain Protein MSCRAMM_SdrD from Staphylococcus aureus Deposited 2023-12-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 244–687（444 aa）	Not recorded	GOL GLYCEROL × 3 EDO 1,2-ETHANEDIOL × 8 CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；0.16 M magnesium chloride, 0.08 TrisHCl pH8.5, 24 %(w/v) PEG4000, 20 % (v/v) glycerol	Resolution 1.80 Å R-free 0.211

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

View Construct and Data Evidence

UniProt name	SDRD_STAAM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–321； UniProt 244–561

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	10pa
Deposition date deposition_date	2026-01-30
最后修订 last_revision	2026-02-11
Structure title title	Crystal structure of SdrD A2-A3 domains from Staphylococcus aureus JH1
Keywords keywords	;SdrD, MSCRAMM, LPXTG-motif, Structural Genomics, PSI-Biology, Center for Structural Biology of Infectious Diseases, CSBID, CELL ADHESION ;; CELL ADHESION
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	24.02 Å
Radius of gyration Rg (electron density) rg_electron	23.23 Å
Forward intensity I(0) i0	22061900.00
Molecular weight molecular_weight	35316.0 kDa
Excluded volume excluded_volume	43974 Å³
Envelope volume envelope_volume	54331 Å³
Hydration-shell volume shell_volume	20579 Å³
Envelope diameter envelope_diameter	82.0 Å
Shell Rg shell_rg	28.67 Å
Envelope Rg envelope_rg	23.22 Å
Shape Rg shape_rg	23.21 Å
Total Rg total_rg	24.01 Å
Total atoms total_atoms	2476
Residues n_residues	317
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	79.5 Å
Rg (real space) rg_real	24.13 Å
Rg uncertainty (real space) rg_real_error	0.77 Å
I(0) (real space) i0_real	2.2060e+07
I(0) uncertainty (real space) i0_real_error	3.4740e+05
Rg (reciprocal space) rg_reciprocal	24.11 Å
I(0) (reciprocal space) i0_reciprocal	22060000.0000
Solution quality estimate total_estimate	0.6180
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.6 Å
Skewness Skewness skewness	0.456
Kurtosis Kurtosis kurtosis	-0.292
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4895000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.844; Stabil: 0.994; Sysdev: 0.203; Positv: 1.000; Valcen: 0.903; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Serine-aspartate repeat-containing protein D
Molecular weight formula_weight	35394.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2574

SNASKNVNDLITSNTTLTVVDADNSKTIVPAQDYLSLKSQITVDDKVKSGDYFTIKYSDTVQVYGLNPEDIKNIGDIKDPNNGETIATAKHDTANNLITYTFTDYVDRFNSVKMGINYSIYMDADTIPVDKKDVPFSVTIGNQITTTTADITYPAYKEADNNSIGSAFTETVSHVGNVEDPGYYNQVVYVNPMDKDLKGAKLKVEAYHPKYPTNIGQINQNVTNIKIYRVPEGYTLNKGYDVNTNDLVDVTDEFKNKMTYGSNQSVNLDFGDITSAYVVMVNTKFQYTNSESPTLVQMATLSSTGNKSVSTGNALGFTNNQ

来源 Source

来源生物 organism	Staphylococcus aureus subsp. aureus JH1
NCBI Class编号 ncbi_taxonomy_id	359787
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	98

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8. Citations (1)

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Unit-cell length a length_a	70.523 Å
Unit-cell length b length_b	73.148 Å
Unit-cell length c length_c	198.705 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	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	orthorhombic

Resolution resolution	1.920 Å
Low-resolution limit resolution_low	36.570 Å
R factor r_factor	0.2139
R_work r_work	0.2121
R_free r_free	0.2449

fit	/app/data/saxs_computation/0p/10pa/10pa.fit
pddf	/app/data/pr_computation/0p/10pa/10pa.pr.out
profile	/app/data/saxs_computation/0p/10pa/10pa.dat

Crystal structure of SdrD A2-A3 domains from Staphylococcus aureus JH1

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

Serine-aspartate repeat-containing protein D

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