SAXSdb — 1bqb

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

PROTEIN (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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–301	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

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 1BQB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7SKL Complex between S. aureus aureolysin and IMPI mutant I57I Deposited 2021-10-21	Different construct Different oligomeric state 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 construct Different oligomeric state 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
7SKM Complex between S. aureus aureolysin and wt IMPI. Deposited 2021-10-21	Different construct Different oligomeric state 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 × 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
7SKM Complex between S. aureus aureolysin and wt IMPI. Deposited 2021-10-21	Different construct Different oligomeric state 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 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

2 other PDB entries and 4 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 1–301

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	1bqb
Deposition date deposition_date	1998-07-14
Structure title title	AUREOLYSIN, STAPHYLOCOCCUS AUREUS METALLOPROTEINASE
Keywords keywords	HYDROLASE, METALLOPROTEINASE; 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	20.39 Å
Radius of gyration Rg (electron density) rg_electron	19.51 Å
Forward intensity I(0) i0	21654500.00
Molecular weight molecular_weight	33489.0 kDa
Excluded volume excluded_volume	40880 Å³
Envelope volume envelope_volume	46524 Å³
Hydration-shell volume shell_volume	20043 Å³
Envelope diameter envelope_diameter	67.5 Å
Shell Rg shell_rg	25.77 Å
Envelope Rg envelope_rg	19.81 Å
Shape Rg shape_rg	19.51 Å
Total Rg total_rg	20.29 Å
Total atoms total_atoms	2358
Residues n_residues	301
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	67.7 Å
Rg (real space) rg_real	20.35 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	2.1650e+07
I(0) uncertainty (real space) i0_real_error	2.9180e+05
Rg (reciprocal space) rg_reciprocal	20.36 Å
I(0) (reciprocal space) i0_reciprocal	21650000.0000
Solution quality estimate total_estimate	0.7223
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.2 Å
Skewness Skewness skewness	0.337
Kurtosis Kurtosis kurtosis	-0.252
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4014000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.819; Stabil: 1.000; Sysdev: 0.319; Positv: 1.000; Valcen: 0.999; Smooth: 0.971

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	PROTEIN (AUREOLYSIN)
Molecular weight formula_weight	33358.8 kDa
EC 编号 ec_number	3.4.24.27
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2518

AAATGTGKGVLGDTKDININSIDGGFSLEDLTHQGKLSAYNFNDQTGQATLITNEDENFVKDDQRAGVDANYYAKQTYDYYKNTFGRESYDNHGSPIVSLTHVNHYGGQDNRNNAAWIGDKMIYGDGDGRTFTNLSGANDVVAHEITHGVTQQTANLEYKDQSGALNESFSDVFGYFVDDEDFLMGEDVYTPGKEGDALRSMSNPEQFGQPSHMKDYVYTEKDNGGVHTNSGIPNKAAYNVIQAIGKSKSEQIYYRALTEYLTSNSNFKDLKDALYQAAKDLYEQQTAEQVYEAWNEVGVE

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	160

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1bqba_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.2 — Thermolysin-like

CATH v4.4 (2 domains)

Domain ID domain_id	1bqbA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	170 — Elastase; domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1bqbA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	390 — Neutral Protease; domain 2
Homologous superfamily homologous superfamily	10 — Neutral Protease Domain 2

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8. Citations (1)

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Unit-cell length a length_a	33.700 Å
Unit-cell length b length_b	79.500 Å
Unit-cell length c length_c	100.100 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.720 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1760
R_work r_work	0.1760
R_free r_free	0.2390

fit	/app/data/saxs_computation/bq/1bqb/1bqb.fit
pddf	/app/data/pr_computation/bq/1bqb/1bqb.pr.out
profile	/app/data/saxs_computation/bq/1bqb/1bqb.dat

AUREOLYSIN, STAPHYLOCOCCUS AUREUS METALLOPROTEINASE

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

PROTEIN (AUREOLYSIN)

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