SAXSdb — 9i6c

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

Alkaline serine protease

Stenotrophomonas maltophilia

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 151–506	Not recorded	Leupeptin × 1 CA CALCIUM ION × 1 SO4 SULFATE ION × 5 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；1.8 M Ammonium sulfate, 0.1 M Tris-HCl	Resolution 2.08 Å R-free 0.218

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 9I6C	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9G8V StmPr1, Stenotrophomonas maltophilia Protease 1, 36 kDa alkine serine protease Deposited 2024-07-24	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 151–506（356 aa）	Not recorded	GOL GLYCEROL × 2 CA CALCIUM ION × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；1.8 M ammonium sulfate 0.1 M Tris	Resolution 1.64 Å R-free 0.209
9GOI StmPr1, Stenotrophomonas maltophilia Protease 1, 36 kDa alkine serine protease in complex with Bortezomib Deposited 2024-09-05	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 151–506（356 aa）	Not recorded	BO2 N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE × 1 GOL GLYCEROL × 4 SO4 SULFATE ION × 3 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293.15 K；0.9 M ammonium sulfate 0.4 M lithium sulfate 0.1 M sodium citrate	Resolution 1.89 Å R-free 0.251
9GRG StmPr1, Stenotrophomonas maltophilia Protease 1, 36 kDa alkine serine protease in complex with PMSF Deposited 2024-09-11	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 151–506（356 aa）	Not recorded	GOL GLYCEROL × 4 PMS phenylmethanesulfonic acid × 1 SO4 SULFATE ION × 4 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293.15 K；0.9 M Ammonium sulfate 0.4 M Lithium sulfate 0.1 M Sodium acetate	Resolution 1.89 Å R-free 0.235
9I67 StmPr1, Stenotrophomonas maltophilia Protease 1, 36 kDa alkine serine protease in complex with Chymostatin Deposited 2025-01-29	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 151–506（356 aa）	Not recorded	CA CALCIUM ION × 1 SO4 SULFATE ION × 6 GOL GLYCEROL × 3 A1I1B (2~{S})-2-[[(1~{S})-1-[(6~{S})-2-azanyl-1,4,5,6-tetrahydropyrimidin-6-yl]-2-[[(2~{S})-4-methyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-phenyl-propan-2-yl]amino]pentan-2-yl]amino]-2-oxidanylidene-ethyl]carbamoylamino]-3-phenyl-propanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 8；293.15 K；1,8 M Ammonium sulfate, 0,1 M Tris-HCl	Resolution 1.99 Å R-free 0.213

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

View Construct and Data Evidence

UniProt name	Q93IQ4_STEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–356； UniProt 151–506

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	9i6c
Deposition date deposition_date	2025-01-29
最后修订 last_revision	2025-08-06
Structure title title	StmPr1, Stenotrophomonas maltophilia Protease 1, 36 kDa alkine serine protease in complex with Leupeptin
Keywords keywords	alkaline serine protease, native, excreted protease, subtilisin-like, 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	19.67 Å
Radius of gyration Rg (electron density) rg_electron	18.49 Å
Forward intensity I(0) i0	26580200.00
Molecular weight molecular_weight	37234.0 kDa
Excluded volume excluded_volume	45531 Å³
Envelope volume envelope_volume	50495 Å³
Hydration-shell volume shell_volume	21987 Å³
Envelope diameter envelope_diameter	62.0 Å
Shell Rg shell_rg	25.65 Å
Envelope Rg envelope_rg	18.75 Å
Shape Rg shape_rg	18.48 Å
Total Rg total_rg	19.37 Å
Total atoms total_atoms	2608
Residues n_residues	358
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	61.0 Å
Rg (real space) rg_real	19.49 Å
Rg uncertainty (real space) rg_real_error	0.29 Å
I(0) (real space) i0_real	2.6580e+07
I(0) uncertainty (real space) i0_real_error	3.2500e+05
Rg (reciprocal space) rg_reciprocal	19.51 Å
I(0) (reciprocal space) i0_reciprocal	26580000.0000
Solution quality estimate total_estimate	0.8930
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.8 Å
Skewness Skewness skewness	0.065
Kurtosis Kurtosis kurtosis	-0.446
Angular range angular_range	— – 0.4050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5358000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.991

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Alkaline serine protease
Molecular weight formula_weight	36231.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2773

LAPNDPYYQQYQWHLHNATGGINAPSAWDVSQGEGVVVAVLDTGILPQHPDLVGNLLEGYDFISDAETSRRATNDRVPGAQDYGDWVENDNECYTGSVAEDSSWHGTHVAGTVAEQTNNGVGMAGVAHKAKVLPVRVLGKCGGYLSDIADAITWASGGTVAGVPANANPAEVINMSLGGSGSCDGTYQDAINGAISRGTTVVVAAGNETDNASKYRPASCDGVVTVGATRITGGITYYSNYGSRVDLSGPGGGGSVDGNPGGYVWQSGSDAATTPESGSYSYMGMGGTSMASPHVAAVAALVQSALIAKGKDPLAPAAMRTLLKETARPFPVSIPTATPIGTGIVDAKAALAKALE

来源 Source

来源生物 organism	Stenotrophomonas maltophilia
NCBI Class编号 ncbi_taxonomy_id	40324
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Leupeptin
Molecular weight formula_weight	412.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

XLLR

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	1

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	165

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8. Citations (1)

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Unit-cell length a length_a	60.780 Å
Unit-cell length b length_b	86.410 Å
Unit-cell length c length_c	132.350 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.080 Å
Low-resolution limit resolution_low	29.640 Å
R factor r_factor	0.1708
R_work r_work	0.1683
R_free r_free	0.2177

fit	/app/data/saxs_computation/i6/9i6c/9i6c.fit
pddf	/app/data/pr_computation/i6/9i6c/9i6c.pr.out
profile	/app/data/saxs_computation/i6/9i6c/9i6c.dat

StmPr1, Stenotrophomonas maltophilia Protease 1, 36 kDa alkine serine protease in complex with Leupeptin

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

Alkaline serine protease

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)