SAXSdb — 4hwx

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

Neutral proteinase inhibitor ScNPI

Streptomyces caespitosus

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 29–141	Not recorded	GOL GLYCEROL × 2 ACT ACETATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；0.1 M sodium citrate dihydrate, 0.2 M ammonium acetate, 10% (w/v) PEG3350, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.90 Å R-free 0.214
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 29–141	Not recorded	GOL GLYCEROL × 2 ACT ACETATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；0.1 M sodium citrate dihydrate, 0.2 M ammonium acetate, 10% (w/v) PEG3350, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.90 Å R-free 0.214

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 4HWX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4HX2 Crystal structure of Streptomyces caespitosus sermetstatin in complex with Bacillus licheniformis subtilisin Deposited 2012-11-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 29–141（113 aa） Chain D 29–141（113 aa）	Not recorded	CA CALCIUM ION × 4 ZN ZINC ION × 2 CL CHLORIDE ION × 1 1AX (2R,2'R)-3,3'-oxydipropane-1,2-diol × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 2 IPA ISOPROPYL ALCOHOL × 3 K POTASSIUM ION × 2 CAC CACODYLATE ION × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1 M cacodylate, 0.2 M zinc acetate dihydrate, 10% (v/v) 2-propanol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.25 Å R-free 0.217
4HX3 Crystal structure of Streptomyces caespitosus sermetstatin in complex with S. caespitosus snapalysin Deposited 2012-11-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 29–141（113 aa） Chain D 29–141（113 aa）	Not recorded	ZN ZINC ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES, 0.2 M magnesium chloride, 15.0% (v/v) ethanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.70 Å R-free 0.242
4HX3 Crystal structure of Streptomyces caespitosus sermetstatin in complex with S. caespitosus snapalysin Deposited 2012-11-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 29–141（113 aa） Chain H 29–141（113 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES, 0.2 M magnesium chloride, 15.0% (v/v) ethanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.70 Å R-free 0.242
4HX3 Crystal structure of Streptomyces caespitosus sermetstatin in complex with S. caespitosus snapalysin Deposited 2012-11-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain J 29–141（113 aa） Chain L 29–141（113 aa）	Not recorded	ZN ZINC ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES, 0.2 M magnesium chloride, 15.0% (v/v) ethanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.70 Å R-free 0.242

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

View Construct and Data Evidence

UniProt name	Q9FDS0_STRCS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–114； UniProt 29–141

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	4hwx
Deposition date deposition_date	2012-11-09
Structure title title	Crystal structure of Streptomyces caespitosus sermetstatin
Keywords keywords	Streptomyces subtilisin inhibitor fold, Hydrolase Inhibitor; Hydrolase Inhibitor
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	15.38 Å
Radius of gyration Rg (electron density) rg_electron	14.38 Å
Forward intensity I(0) i0	3268890.00
Molecular weight molecular_weight	12181.0 kDa
Excluded volume excluded_volume	14989 Å³
Envelope volume envelope_volume	17541 Å³
Hydration-shell volume shell_volume	10904 Å³
Envelope diameter envelope_diameter	51.3 Å
Shell Rg shell_rg	19.34 Å
Envelope Rg envelope_rg	14.74 Å
Shape Rg shape_rg	14.37 Å
Total Rg total_rg	15.40 Å
Total atoms total_atoms	852
Residues n_residues	113
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	50.8 Å
Rg (real space) rg_real	15.35 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	3.2690e+06
I(0) uncertainty (real space) i0_real_error	3.8020e+04
Rg (reciprocal space) rg_reciprocal	15.35 Å
I(0) (reciprocal space) i0_reciprocal	3269000.0000
Solution quality estimate total_estimate	0.8879
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	50.2 Å
Skewness Skewness skewness	0.277
Kurtosis Kurtosis kurtosis	-0.339
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	490800.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.953

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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	Neutral proteinase inhibitor ScNPI
Molecular weight formula_weight	11923.4 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	978

GSAHGPSAMVFTVIQGSGEPTDTVLRATTLSCAYTAEGTHPAPRAACDALNATDGELNRLLAAPDPSLVCPMYFDPVTVTADGVLNGRRVAWKHTFSNTCVMSANLNSNPVYAF

来源 Source

来源生物 organism	Streptomyces caespitosus
NCBI Class编号 ncbi_taxonomy_id	53502
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 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	126

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4hwxa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.84 — Subtilisin inhibitor
Superfamily Superfamily superfamily	d.84.1 — Subtilisin inhibitor
Family Family family	d.84.1.0 — automated matches

Domain ID domain_id	d4hwxa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	4hwxA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	350 — Subtilisin Inhibitor
Homologous superfamily homologous superfamily	10 — Subtilisin inhibitor-like

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8. Citations (1)

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Unit-cell length a length_a	71.040 Å
Unit-cell length b length_b	71.040 Å
Unit-cell length c length_c	52.400 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	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	39.890 Å
R factor r_factor	0.1883
R_work r_work	0.1870
R_free r_free	0.2140

fit	/app/data/saxs_computation/hw/4hwx/4hwx.fit
pddf	/app/data/pr_computation/hw/4hwx/4hwx.pr.out
profile	/app/data/saxs_computation/hw/4hwx/4hwx.dat

Crystal structure of Streptomyces caespitosus sermetstatin

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

Neutral proteinase inhibitor ScNPI

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