SAXSdb — 7skm

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

Zinc metalloproteinase aureolysin

OrganismNot specified

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 209–509	Not recorded	IMPI alpha × 1 （P82176） IMPI alpha × 1 （P82176） CA CALCIUM ION × 3 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；Best crystals of aureolysin in complex with either IMPI variant were obtained at 20 degrees with protein solutions consisting of 5 mg/mL of aureolysin and 2.9 mg/mL of IMPI (peptidase:inhibitor molar ratio of 1:2.5) in 50 mM Tris-HCl, 150 mM sodium chloride, 1.6 mM calcium chloride, 8.3 microM zinc chloride, pH 8.0, which was mixed with reservoir solution comprising 0.1 M Bis-Tris, 25% (w/v) PEG 3350, pH 5.5.	Resolution 1.85 Å R-free 0.219
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 209–509	Not recorded	IMPI alpha × 1 （P82176） IMPI alpha × 1 （P82176） CA CALCIUM ION × 3 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；Best crystals of aureolysin in complex with either IMPI variant were obtained at 20 degrees with protein solutions consisting of 5 mg/mL of aureolysin and 2.9 mg/mL of IMPI (peptidase:inhibitor molar ratio of 1:2.5) in 50 mM Tris-HCl, 150 mM sodium chloride, 1.6 mM calcium chloride, 8.3 microM zinc chloride, pH 8.0, which was mixed with reservoir solution comprising 0.1 M Bis-Tris, 25% (w/v) PEG 3350, pH 5.5.	Resolution 1.85 Å R-free 0.219

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 7SKM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BQB AUREOLYSIN, STAPHYLOCOCCUS AUREUS METALLOPROTEINASE Deposited 1998-07-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–301（301 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.2；0.1 M SODIUM ACETATE PH 5.2 AND 40% PEG 4000	Resolution 1.72 Å R-free 0.239
7SKL Complex between S. aureus aureolysin and IMPI mutant I57I Deposited 2021-10-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 209–509（301 aa）	Not recorded	CA CALCIUM ION × 3 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Best crystals of aureolysin in complex with IMPI mutant I57F were obtained at 20 dgrees with protein solutions consisting of 5 mg/mL of aureolysin and 2.9 mg/mL of IMPI (peptidase:inhibitor molar ratio of 1:2.5) in 50 mM Tris-HCl, 150 mM sodium chloride, 1.6 mM calcium chloride, 8.3 microM zinc chloride, pH 8.0, which was mixed with reservoir solution comprising 0.1 M Bis-Tris, 25% (w/v) PEG 3350, pH 5.5.	Resolution 1.60 Å R-free 0.188
7SKL Complex between S. aureus aureolysin and IMPI mutant I57I Deposited 2021-10-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 209–509（301 aa）	Not recorded	CA CALCIUM ION × 3 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Best crystals of aureolysin in complex with IMPI mutant I57F were obtained at 20 dgrees with protein solutions consisting of 5 mg/mL of aureolysin and 2.9 mg/mL of IMPI (peptidase:inhibitor molar ratio of 1:2.5) in 50 mM Tris-HCl, 150 mM sodium chloride, 1.6 mM calcium chloride, 8.3 microM zinc chloride, pH 8.0, which was mixed with reservoir solution comprising 0.1 M Bis-Tris, 25% (w/v) PEG 3350, pH 5.5.	Resolution 1.60 Å R-free 0.188

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AURE_STAAU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–301； UniProt 209–509 Author chain C； PDBConstruct 1–301； UniProt 209–509

IMPI alpha

Galleria mellonella

UniProt P82176

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 19–56 Chain E； UniProt 57–88	Not recorded	Zinc metalloproteinase aureolysin × 1 （P81177） CA CALCIUM ION × 3 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；Best crystals of aureolysin in complex with either IMPI variant were obtained at 20 degrees with protein solutions consisting of 5 mg/mL of aureolysin and 2.9 mg/mL of IMPI (peptidase:inhibitor molar ratio of 1:2.5) in 50 mM Tris-HCl, 150 mM sodium chloride, 1.6 mM calcium chloride, 8.3 microM zinc chloride, pH 8.0, which was mixed with reservoir solution comprising 0.1 M Bis-Tris, 25% (w/v) PEG 3350, pH 5.5.	Resolution 1.85 Å R-free 0.219
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 19–56 Chain F； UniProt 57–88	Not recorded	Zinc metalloproteinase aureolysin × 1 （P81177） CA CALCIUM ION × 3 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；Best crystals of aureolysin in complex with either IMPI variant were obtained at 20 degrees with protein solutions consisting of 5 mg/mL of aureolysin and 2.9 mg/mL of IMPI (peptidase:inhibitor molar ratio of 1:2.5) in 50 mM Tris-HCl, 150 mM sodium chloride, 1.6 mM calcium chloride, 8.3 microM zinc chloride, pH 8.0, which was mixed with reservoir solution comprising 0.1 M Bis-Tris, 25% (w/v) PEG 3350, pH 5.5.	Resolution 1.85 Å R-free 0.219

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 7SKM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3SSB Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin Deposited 2011-07-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 19–56（38 aa） Fragment：UNP residues 19-56 Chain I 57–88（32 aa） Fragment：UNP residues 57-88	Not recorded	GOL GLYCEROL × 2 ZN ZINC ION × 1 CA CALCIUM ION × 3 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；20% w/v PEG 4000, 0.2 M sodium acetate, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.193
3SSB Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin Deposited 2011-07-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 19–56（38 aa） Fragment：UNP residues 19-56 Chain J 57–88（32 aa） Fragment：UNP residues 57-88	Not recorded	GOL GLYCEROL × 1 ZN ZINC ION × 1 CA CALCIUM ION × 3 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；20% w/v PEG 4000, 0.2 M sodium acetate, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.193
7SKL Complex between S. aureus aureolysin and IMPI mutant I57I Deposited 2021-10-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 19–56（38 aa） Chain E 57–88（32 aa）	Mutation：I57F	CA CALCIUM ION × 3 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Best crystals of aureolysin in complex with IMPI mutant I57F were obtained at 20 dgrees with protein solutions consisting of 5 mg/mL of aureolysin and 2.9 mg/mL of IMPI (peptidase:inhibitor molar ratio of 1:2.5) in 50 mM Tris-HCl, 150 mM sodium chloride, 1.6 mM calcium chloride, 8.3 microM zinc chloride, pH 8.0, which was mixed with reservoir solution comprising 0.1 M Bis-Tris, 25% (w/v) PEG 3350, pH 5.5.	Resolution 1.60 Å R-free 0.188
7SKL Complex between S. aureus aureolysin and IMPI mutant I57I Deposited 2021-10-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 19–56（38 aa） Chain F 57–88（32 aa）	Mutation：I57F	CA CALCIUM ION × 3 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Best crystals of aureolysin in complex with IMPI mutant I57F were obtained at 20 dgrees with protein solutions consisting of 5 mg/mL of aureolysin and 2.9 mg/mL of IMPI (peptidase:inhibitor molar ratio of 1:2.5) in 50 mM Tris-HCl, 150 mM sodium chloride, 1.6 mM calcium chloride, 8.3 microM zinc chloride, pH 8.0, which was mixed with reservoir solution comprising 0.1 M Bis-Tris, 25% (w/v) PEG 3350, pH 5.5.	Resolution 1.60 Å R-free 0.188

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IMPI_GALME
Isoform	—
PDB entities	2, 3
Chains and sequence ranges	Author chain B； PDBConstruct 3–40； UniProt 19–56 Author chain D； PDBConstruct 3–40； UniProt 19–56 Author chain E； PDBConstruct 1–32； UniProt 57–88 Author chain F； PDBConstruct 1–32； UniProt 57–88

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	7skm
Deposition date deposition_date	2021-10-21
Structure title title	Complex between S. aureus aureolysin and wt IMPI.
Keywords keywords	Metallopeptidase, inhibitor complex, point mutant, HYDROLASE; HYDROLASE
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	29.27 Å
Radius of gyration Rg (electron density) rg_electron	28.74 Å
Forward intensity I(0) i0	122840000.00
Molecular weight molecular_weight	81918.0 kDa
Excluded volume excluded_volume	99826 Å³
Envelope volume envelope_volume	124240 Å³
Hydration-shell volume shell_volume	35898 Å³
Envelope diameter envelope_diameter	101.5 Å
Shell Rg shell_rg	36.13 Å
Envelope Rg envelope_rg	28.61 Å
Shape Rg shape_rg	28.75 Å
Total Rg total_rg	29.37 Å
Total atoms total_atoms	5742
Residues n_residues	734
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	95.1 Å
Rg (real space) rg_real	29.24 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	1.2280e+08
I(0) uncertainty (real space) i0_real_error	1.6570e+06
Rg (reciprocal space) rg_reciprocal	29.25 Å
I(0) (reciprocal space) i0_reciprocal	122800000.0000
Solution quality estimate total_estimate	0.9006
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.2 Å
Skewness Skewness skewness	0.290
Kurtosis Kurtosis kurtosis	-0.423
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	29450000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.976

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Zinc metalloproteinase aureolysin
Molecular weight formula_weight	33336.7 kDa
EC 编号 ec_number	3.4.24.29
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	6467

AAATGTGKGVLGDTKDININSIDGGFSLEDLTHQGKLSAYNFNDQTGQATLITNEDENFVKDDQRAGVDANYYAKQTYDYYKNTFGRESYDNHGSPIVSLTHVNHYGGQDNRNNAAWIGDKMIYGDGDGRTFTNLSGANDVVAHELTHGVTQETANLEYKDQSGALNESFSDVFGYFVDDEDFLMGEDVYTPGKEGDALRSMSNPEQFGQPSHMKDYVYTEKDNGGVHTNSGIPNKAAYNVIQAIGKSKSEQIYYRALTEYLTSNSNFKDCKDALYQAAKDLYDEQTAEQVYEAWNEVGVE

Entity 2 Entity 2 polymer

Description description	IMPI alpha
Molecular weight formula_weight	4286.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

GMSIVLICNGGHEYYECGGACDNVCADLHIQNKTNCPIIN

来源 Source

来源生物 organism	Galleria mellonella
通用名 common_name	Greater wax moth
NCBI Class编号 ncbi_taxonomy_id	7137
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	IMPI alpha
Molecular weight formula_weight	3684.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

IRCNDKCYCEDGYARDVNGKCIPIKDCPKIRS

来源 Source

来源生物 organism	Galleria mellonella
通用名 common_name	Greater wax moth
NCBI Class编号 ncbi_taxonomy_id	7137
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 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 7 Entity 7 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	709

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8. Citations (2)

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Unit-cell length a length_a	68.140 Å
Unit-cell length b length_b	68.140 Å
Unit-cell length c length_c	166.180 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	P 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	52.689 Å
R factor r_factor	—
R_work r_work	0.1644
R_free r_free	0.2186

fit	/app/data/saxs_computation/sk/7skm/7skm.fit
pddf	/app/data/pr_computation/sk/7skm/7skm.pr.out
profile	/app/data/saxs_computation/sk/7skm/7skm.dat

Complex between S. aureus aureolysin and wt IMPI.

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

Zinc metalloproteinase aureolysin

State in the Current Structure

Other States of the Same Protein in the Database

IMPI alpha

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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)