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1yn4

Crystal Structures of EAP Domains from Staphylococcus aureus Reveal an Unexpected Homology to Bacterial Superantigens

Method: X-RAY DIFFRACTION Dmax: 45.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

EapH1

Staphylococcus aureus

UniProt Q99S64

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 43–141 Fragment：residues 43-141 Mutation：K70A, K71A, Q75A, Q100A, K120A, K125A, K141A ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.7；293 K；PEG 8000, zinc acetate, cacodylate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.80 Å R-free 0.238

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 1YN4 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4NZL Extracellular proteins of Staphylococcus aureus inhibit the neutrophil serine proteases Deposited 2013-12-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 43–141（99 aa） Fragment：unp residues 43-141
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；298 K；1.0 M succinic acid, 0.1 M Na-HEPES, 1% (w/v) PEG 2000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.85 Å R-free 0.207

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

View Construct and Data Evidence
UniProt name Q99S64_STAAM
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–99； UniProt 43–141

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 1yn4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1yn4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1yn4
Deposition date deposition_date2005-01-23
Structure title titleCrystal Structures of EAP Domains from Staphylococcus aureus Reveal an Unexpected Homology to Bacterial Superantigens
Keywords keywordsVirulence factor, Toxin, Extracellular adherence protein, Staphylococcus aureus, UNKNOWN FUNCTION; UNKNOWN FUNCTION
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_guinier14.51 Å
Radius of gyration Rg (electron density) rg_electron12.92 Å
Forward intensity I(0) i02534510.00
Molecular weight molecular_weight10815.0 kDa
Excluded volume excluded_volume13469 ų
Envelope volume envelope_volume15120 ų
Hydration-shell volume shell_volume10244 ų
Envelope diameter envelope_diameter42.6 Å
Shell Rg shell_rg18.34 Å
Envelope Rg envelope_rg13.12 Å
Shape Rg shape_rg12.86 Å
Total Rg total_rg14.31 Å
Total atoms total_atoms756
Residues n_residues99
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 dmax45.0 Å
Rg (real space) rg_real14.42 Å
Rg uncertainty (real space) rg_real_error0.24 Å
I(0) (real space) i0_real2.5350e+06
I(0) uncertainty (real space) i0_real_error2.5920e+04
Rg (reciprocal space) rg_reciprocal14.43 Å
I(0) (reciprocal space) i0_reciprocal2535000.0000
Solution quality estimate total_estimate0.8961
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary44.4 Å
Skewness Skewness skewness0.112
Kurtosis Kurtosis kurtosis-0.407
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha253000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.943
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id1yn4A00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily120 —
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8. Citations (1)

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9. Files and Curves (10)