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10ps

Crystal structure of SdrD A2-A3-B1-B2 domains from Staphylococcus aureus JH1

Method: X-RAY DIFFRACTION Dmax: 154.6 Å Quality: REASONABLE
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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

UniProt Q99W47

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 244–798 Fragment：A2-A3-B1-B2 domains 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

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 10PS Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
10PA Crystal structure of SdrD A2-A3 domains from Staphylococcus aureus JH1 Deposited 2026-01-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 244–561（318 aa） Fragment：A2-A3 domains
Not recorded 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
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 4–558； UniProt 244–798

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.

SAXS scattering curve SAXS Profile

SAXS profile for 10ps

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 10ps
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2. Structure Basics 2. Structure Basics

Entry ID entry_id10ps
Deposition date deposition_date2026-01-31
最后修订 last_revision2026-02-11
Structure title titleCrystal structure of SdrD A2-A3-B1-B2 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 methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier38.59 Å
Radius of gyration Rg (electron density) rg_electron39.89 Å
Forward intensity I(0) i063153000.00
Molecular weight molecular_weight61812.0 kDa
Excluded volume excluded_volume76581 ų
Envelope volume envelope_volume109260 ų
Hydration-shell volume shell_volume27296 ų
Envelope diameter envelope_diameter161.2 Å
Shell Rg shell_rg36.90 Å
Envelope Rg envelope_rg41.13 Å
Shape Rg shape_rg39.89 Å
Total Rg total_rg39.67 Å
Total atoms total_atoms4333
Residues n_residues556
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax154.6 Å
Rg (real space) rg_real39.75 Å
Rg uncertainty (real space) rg_real_error2.57 Å
I(0) (real space) i0_real6.3150e+07
I(0) uncertainty (real space) i0_real_error1.3240e+06
Rg (reciprocal space) rg_reciprocal39.03 Å
I(0) (reciprocal space) i0_reciprocal63110000.0000
Solution quality estimate total_estimate0.6834
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.4 Å
Skewness Skewness skewness0.784
Kurtosis Kurtosis kurtosis0.042
Angular range angular_range— – 0.2050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3518000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.270; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.109; Smooth: 0.962
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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8. Citations (1)

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9. Files and Curves (10)