8d4o

Crystal Structure of the Neutrophil Serine Protease Inhibitor Eap1 from S. aureus

Method: X-RAY DIFFRACTION D_max: 78.6 Å Quality: GOOD

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

Extracellular Adherence 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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 49–145	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 49–145	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
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 49–145	Not recorded	No other associated polymer	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
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 49–145	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

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 8D4O	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1YN3 Crystal Structures of EAP Domains from Staphylococcus aureus Reveal an Unexpected Homology to Bacterial Superantigens Deposited 2005-01-23	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 160–254（95 aa） Fragment：residues 160-254	Mutation：V253I	No recorded non-water small molecule	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
1YN3 Crystal Structures of EAP Domains from Staphylococcus aureus Reveal an Unexpected Homology to Bacterial Superantigens Deposited 2005-01-23	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 160–254（95 aa） Fragment：residues 160-254	Mutation：V253I	No recorded non-water small molecule	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
8D4Q Crystal Structure of Neutrophil Elastase Inhibited by Eap1 from S. aureus Deposited 2022-06-02	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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MAP_STAAM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–100； UniProt 49–145 Author chain B； PDBConstruct 4–100； UniProt 49–145 Author chain C； PDBConstruct 4–100； UniProt 49–145 Author chain D； PDBConstruct 4–100； UniProt 49–145

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	8d4o
Deposition date deposition_date	2022-06-02
Structure title title	Crystal Structure of the Neutrophil Serine Protease Inhibitor Eap1 from S. aureus
Keywords keywords	Protease Inhibitor, Immune Evasion, Neutrophil, S. aureus, PROTEIN BINDING; 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	23.80 Å
Radius of gyration Rg (electron density) rg_electron	22.77 Å
Forward intensity I(0) i0	32144600.00
Molecular weight molecular_weight	44498.0 kDa
Excluded volume excluded_volume	56290 Å³
Envelope volume envelope_volume	68526 Å³
Hydration-shell volume shell_volume	25417 Å³
Envelope diameter envelope_diameter	80.9 Å
Shell Rg shell_rg	29.79 Å
Envelope Rg envelope_rg	22.99 Å
Shape Rg shape_rg	22.76 Å
Total Rg total_rg	23.72 Å
Total atoms total_atoms	3136
Residues n_residues	396
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	78.6 Å
Rg (real space) rg_real	23.76 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	3.2140e+07
I(0) uncertainty (real space) i0_real_error	4.6900e+05
Rg (reciprocal space) rg_reciprocal	23.77 Å
I(0) (reciprocal space) i0_reciprocal	32140000.0000
Solution quality estimate total_estimate	0.8004
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	29.5 Å
Skewness Skewness skewness	0.345
Kurtosis Kurtosis kurtosis	-0.233
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10970000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.804; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

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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	Extracellular Adherence Protein
Molecular weight formula_weight	11185.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	3651

GSTIQIPYTITVNGTSQNILSSLTFNKNQNISYKDIENKVKSVLYFNRGISDIDLRLSKQAEYTVHFKNGTKRVIDLKSGIYTADLINTSDIKAISVNVD

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	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	515

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8. Citations (1)

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Unit-cell length a length_a	37.623 Å
Unit-cell length b length_b	48.091 Å
Unit-cell length c length_c	55.161 Å
Unit-cell angle α angle_alpha	84.26 °
Unit-cell angle β angle_beta	89.92 °
Unit-cell angle γ angle_gamma	72.96 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	37.080 Å
R factor r_factor	0.1696
R_work r_work	0.1686
R_free r_free	0.1974

fit	/app/data/saxs_computation/d4/8d4o/8d4o.fit
pddf	/app/data/pr_computation/d4/8d4o/8d4o.pr.out
profile	/app/data/saxs_computation/d4/8d4o/8d4o.dat