1yn3

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

Method: X-RAY DIFFRACTION D_max: 151.6 Å Quality: REASONABLE

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

truncated cell surface protein map-w

Staphylococcus aureus

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 160–254	Fragment：residues 160-254 Mutation：V253I	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；PEG 8000, ammonium sulfate, MES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 1.35 Å R-free 0.230
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 160–254	Fragment：residues 160-254 Mutation：V253I	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；PEG 8000, ammonium sulfate, MES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 1.35 Å R-free 0.230

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 1YN3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8D4O Crystal Structure of the Neutrophil Serine Protease Inhibitor Eap1 from S. aureus Deposited 2022-06-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 49–145（97 aa）	Not recorded	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium acetate trihydrate, 2.0 M sodium chloride	Resolution 1.45 Å R-free 0.197
8D4O Crystal Structure of the Neutrophil Serine Protease Inhibitor Eap1 from S. aureus Deposited 2022-06-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 49–145（97 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium acetate trihydrate, 2.0 M sodium chloride	Resolution 1.45 Å R-free 0.197
8D4O Crystal Structure of the Neutrophil Serine Protease Inhibitor Eap1 from S. aureus Deposited 2022-06-02	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 49–145（97 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium acetate trihydrate, 2.0 M sodium chloride	Resolution 1.45 Å R-free 0.197
8D4O Crystal Structure of the Neutrophil Serine Protease Inhibitor Eap1 from S. aureus Deposited 2022-06-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 49–145（97 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium acetate trihydrate, 2.0 M sodium chloride	Resolution 1.45 Å R-free 0.197
8D4Q Crystal Structure of Neutrophil Elastase Inhibited by Eap1 from S. aureus Deposited 2022-06-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 49–145（97 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；0.1M sodium citrate (pH 5.2), 12% (w/v) PEG-6000	Resolution 2.20 Å R-free 0.217
8D4Q Crystal Structure of Neutrophil Elastase Inhibited by Eap1 from S. aureus Deposited 2022-06-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 49–145（97 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；0.1M sodium citrate (pH 5.2), 12% (w/v) PEG-6000	Resolution 2.20 Å R-free 0.217
8D4S Crystal Structure of Cathepsin G Inhibited by Eap1 from S. aureus Deposited 2022-06-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 49–145（97 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1M BisTris (pH 5.5), 0.2M Magnesium Chloride, 25% (w/v) PEG-3350	Resolution 1.95 Å R-free 0.261
8D4S Crystal Structure of Cathepsin G Inhibited by Eap1 from S. aureus Deposited 2022-06-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 49–145（97 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1M BisTris (pH 5.5), 0.2M Magnesium Chloride, 25% (w/v) PEG-3350	Resolution 1.95 Å R-free 0.261
8D4S Crystal Structure of Cathepsin G Inhibited by Eap1 from S. aureus Deposited 2022-06-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 49–145（97 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1M BisTris (pH 5.5), 0.2M Magnesium Chloride, 25% (w/v) PEG-3350	Resolution 1.95 Å R-free 0.261
8D4S Crystal Structure of Cathepsin G Inhibited by Eap1 from S. aureus Deposited 2022-06-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 49–145（97 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1M BisTris (pH 5.5), 0.2M Magnesium Chloride, 25% (w/v) PEG-3350	Resolution 1.95 Å R-free 0.261
8D4U Crystal Structure of Neutrophil Elastase Inhibited by Eap2 from S. aureus Deposited 2022-06-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 158–254（97 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M HEPES (pH 7.5), 0.2M Lithium Sulfate, 25%(w/v) PEG-3350	Resolution 1.90 Å R-free 0.230
8D4U Crystal Structure of Neutrophil Elastase Inhibited by Eap2 from S. aureus Deposited 2022-06-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 158–254（97 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M HEPES (pH 7.5), 0.2M Lithium Sulfate, 25%(w/v) PEG-3350	Resolution 1.90 Å R-free 0.230
8D4V Crystal Structure of Cathepsin G Inhibited by Eap2 from S. aureus Deposited 2022-06-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 158–254（97 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M BisTris (pH 6.5), 0.2M Ammonium Sulfate, 25%(w/v) PEG-3350	Resolution 1.85 Å R-free 0.251
8D4V Crystal Structure of Cathepsin G Inhibited by Eap2 from S. aureus Deposited 2022-06-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 158–254（97 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M BisTris (pH 6.5), 0.2M Ammonium Sulfate, 25%(w/v) PEG-3350	Resolution 1.85 Å R-free 0.251
8D7I Bifunctional Inhibition of Neutrophil Elastase and Cathepsin G by Eap1 from S. aureus Deposited 2022-06-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 49–145（97 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；0.1M BisTris, 0.2M sodium/potassium tartrate, 14% PEG-8000	Resolution 3.63 Å R-free 0.217
8D7I Bifunctional Inhibition of Neutrophil Elastase and Cathepsin G by Eap1 from S. aureus Deposited 2022-06-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 49–145（97 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；0.1M BisTris, 0.2M sodium/potassium tartrate, 14% PEG-8000	Resolution 3.63 Å R-free 0.217
8D7I Bifunctional Inhibition of Neutrophil Elastase and Cathepsin G by Eap1 from S. aureus Deposited 2022-06-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 49–145（97 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；0.1M BisTris, 0.2M sodium/potassium tartrate, 14% PEG-8000	Resolution 3.63 Å R-free 0.217
8D7I Bifunctional Inhibition of Neutrophil Elastase and Cathepsin G by Eap1 from S. aureus Deposited 2022-06-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 49–145（97 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；0.1M BisTris, 0.2M sodium/potassium tartrate, 14% PEG-8000	Resolution 3.63 Å R-free 0.217
8D7I Bifunctional Inhibition of Neutrophil Elastase and Cathepsin G by Eap1 from S. aureus Deposited 2022-06-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain N 49–145（97 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；0.1M BisTris, 0.2M sodium/potassium tartrate, 14% PEG-8000	Resolution 3.63 Å R-free 0.217
8D7I Bifunctional Inhibition of Neutrophil Elastase and Cathepsin G by Eap1 from S. aureus Deposited 2022-06-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain Q 49–145（97 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；0.1M BisTris, 0.2M sodium/potassium tartrate, 14% PEG-8000	Resolution 3.63 Å R-free 0.217
8D7K Bifunctional Inhibition of Neutrophil Elastase and Cathepsin G by Eap2 from S. aureus Deposited 2022-06-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 158–254（97 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.6；293 K；0.1M Citric acid, 0.15M Lithium Sulfate, 12% PEG-6000	Resolution 3.10 Å R-free 0.258
8D7K Bifunctional Inhibition of Neutrophil Elastase and Cathepsin G by Eap2 from S. aureus Deposited 2022-06-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 158–254（97 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.6；293 K；0.1M Citric acid, 0.15M Lithium Sulfate, 12% PEG-6000	Resolution 3.10 Å R-free 0.258
8D7K Bifunctional Inhibition of Neutrophil Elastase and Cathepsin G by Eap2 from S. aureus Deposited 2022-06-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 158–254（97 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.6；293 K；0.1M Citric acid, 0.15M Lithium Sulfate, 12% PEG-6000	Resolution 3.10 Å R-free 0.258
8D7K Bifunctional Inhibition of Neutrophil Elastase and Cathepsin G by Eap2 from S. aureus Deposited 2022-06-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 158–254（97 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.6；293 K；0.1M Citric acid, 0.15M Lithium Sulfate, 12% PEG-6000	Resolution 3.10 Å R-free 0.258
9ASS Crystal Structure of Neutrophil Elastase Inhibited by Eap4 from S. aureus Deposited 2024-02-26	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 C 372–476（105 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.01 M zinc sulfate heptahydrate 0.1M MES (pH 6.5) 25% (v/v) peg-550MME	Resolution 1.75 Å R-free 0.212
9ASX BIFUNCTIONAL INHIBITION OF NEUTROPHIL ELASTASE AND CATHEPSIN G by Eap3 of S. aureus Deposited 2024-02-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 267–363（97 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M ammonium citrate 0.1 M imidazole (pH 6.8) 22% (w/v) peg-2kMME	Resolution 1.96 Å R-free 0.228
9ATK BIFUNCTIONAL INHIBITION OF NEUTROPHIL ELASTASE AND CATHEPSIN G by Eap4 of S. aureus Deposited 2024-02-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 372–476（105 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium citrate (pH 5.5) 12% (w/v) PEG-6K	Resolution 2.11 Å R-free 0.233
9ATK BIFUNCTIONAL INHIBITION OF NEUTROPHIL ELASTASE AND CATHEPSIN G by Eap4 of S. aureus Deposited 2024-02-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 372–476（105 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium citrate (pH 5.5) 12% (w/v) PEG-6K	Resolution 2.11 Å R-free 0.233
9ATK BIFUNCTIONAL INHIBITION OF NEUTROPHIL ELASTASE AND CATHEPSIN G by Eap4 of S. aureus Deposited 2024-02-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 372–476（105 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium citrate (pH 5.5) 12% (w/v) PEG-6K	Resolution 2.11 Å R-free 0.233
9ATK BIFUNCTIONAL INHIBITION OF NEUTROPHIL ELASTASE AND CATHEPSIN G by Eap4 of S. aureus Deposited 2024-02-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 372–476（105 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium citrate (pH 5.5) 12% (w/v) PEG-6K	Resolution 2.11 Å R-free 0.233
9ATU Bifunctional Inhibition of Neutrophil Elastase by Eap4 from S. aureus Deposited 2024-02-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 372–476（105 aa） Chain E 372–476（105 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M ammonium acetate 0.1 M Tris-HCl (pH 8.0) 17% (w/v) PEG-10K	Resolution 2.05 Å R-free 0.237
9ATU Bifunctional Inhibition of Neutrophil Elastase by Eap4 from S. aureus Deposited 2024-02-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 372–476（105 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M ammonium acetate 0.1 M Tris-HCl (pH 8.0) 17% (w/v) PEG-10K	Resolution 2.05 Å R-free 0.237
9ATU Bifunctional Inhibition of Neutrophil Elastase by Eap4 from S. aureus Deposited 2024-02-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 372–476（105 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M ammonium acetate 0.1 M Tris-HCl (pH 8.0) 17% (w/v) PEG-10K	Resolution 2.05 Å R-free 0.237
9ATU Bifunctional Inhibition of Neutrophil Elastase by Eap4 from S. aureus Deposited 2024-02-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 372–476（105 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M ammonium acetate 0.1 M Tris-HCl (pH 8.0) 17% (w/v) PEG-10K	Resolution 2.05 Å R-free 0.237
9ATU Bifunctional Inhibition of Neutrophil Elastase by Eap4 from S. aureus Deposited 2024-02-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 6 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 372–476（105 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M ammonium acetate 0.1 M Tris-HCl (pH 8.0) 17% (w/v) PEG-10K	Resolution 2.05 Å R-free 0.237

11 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MAP1_STAAM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–98； UniProt 160–254 Author chain B； PDBConstruct 4–98； UniProt 160–254

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1yn3
Deposition date deposition_date	2005-01-23
Structure title title	Crystal Structures of EAP Domains from Staphylococcus aureus Reveal an Unexpected Homology to Bacterial Superantigens
Keywords keywords	Virulence-factor, Toxin, Extracellular-adherence protein, Staphylococcus, PROTEIN BINDING; TOXIN, PROTEIN BINDING
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	40.72 Å
Radius of gyration Rg (electron density) rg_electron	40.88 Å
Forward intensity I(0) i0	7022020.00
Molecular weight molecular_weight	21605.0 kDa
Excluded volume excluded_volume	27201 Å³
Envelope volume envelope_volume	46137 Å³
Hydration-shell volume shell_volume	9380 Å³
Envelope diameter envelope_diameter	114.2 Å
Shell Rg shell_rg	48.61 Å
Envelope Rg envelope_rg	37.42 Å
Shape Rg shape_rg	40.89 Å
Total Rg total_rg	41.38 Å
Total atoms total_atoms	1520
Residues n_residues	196
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	151.6 Å
Rg (real space) rg_real	41.15 Å
Rg uncertainty (real space) rg_real_error	3.07 Å
I(0) (real space) i0_real	7.0220e+06
I(0) uncertainty (real space) i0_real_error	1.4740e+05
Rg (reciprocal space) rg_reciprocal	40.73 Å
I(0) (reciprocal space) i0_reciprocal	7019000.0000
Solution quality estimate total_estimate	0.5389
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	4
Primary peak position r_peak_primary	15.5 Å
Skewness Skewness skewness	0.081
Kurtosis Kurtosis kurtosis	-1.709
Angular range angular_range	— – 0.1950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	245500.0000
Real-space data points n_real_points	40
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.000; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.001; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	1yn3A00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	1yn3B00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	120 —

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8. Citations (1)

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Unit-cell length a length_a	64.116 Å
Unit-cell length b length_b	64.116 Å
Unit-cell length c length_c	141.706 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	1.350 Å
Low-resolution limit resolution_low	29.870 Å
R factor r_factor	0.2180
R_work r_work	0.2180
R_free r_free	0.2300

Description description	truncated cell surface protein map-w
Molecular weight formula_weight	10810.2 kDa
Mutation mutation	V253I
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1824

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

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

truncated cell surface protein map-w

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Staphylococcus aureus
NCBI Class编号 ncbi_taxonomy_id	1280
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	304

fit	/app/data/saxs_computation/yn/1yn3/1yn3.fit
pddf	/app/data/pr_computation/yn/1yn3/1yn3.pr.out
profile	/app/data/saxs_computation/yn/1yn3/1yn3.dat