SAXSdb — 1dki

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

PYROGENIC EXOTOXIN B ZYMOGEN

Streptococcus pyogenes

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 28–398	Fragment：STREPTOCOCCAL PYROGENIC EXOTOXIN ZYMOGEN Mutation：C47S	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.4；298 K；0.2M Ammonium sulfate, 0.1M Formic acid pH4.2, 16%PEG4000, 4%PEG8000, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.245
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 28–398	Fragment：STREPTOCOCCAL PYROGENIC EXOTOXIN ZYMOGEN Mutation：C47S	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.4；298 K；0.2M Ammonium sulfate, 0.1M Formic acid pH4.2, 16%PEG4000, 4%PEG8000, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.245
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 28–398	Fragment：STREPTOCOCCAL PYROGENIC EXOTOXIN ZYMOGEN Mutation：C47S	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.4；298 K；0.2M Ammonium sulfate, 0.1M Formic acid pH4.2, 16%PEG4000, 4%PEG8000, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.245
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 28–398	Fragment：STREPTOCOCCAL PYROGENIC EXOTOXIN ZYMOGEN Mutation：C47S	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.4；298 K；0.2M Ammonium sulfate, 0.1M Formic acid pH4.2, 16%PEG4000, 4%PEG8000, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.245

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 1DKI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1PVJ Crystal structure of the Streptococcal pyrogenic exotoxin B (SpeB)- inhibitor complex Deposited 2003-06-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 31–398（368 aa） Fragment：Streptococcal Pyrogenic Exotoxin B (SpeB) Chain B 31–398（368 aa） Fragment：Streptococcal Pyrogenic Exotoxin B (SpeB) Chain C 31–398（368 aa） Fragment：Streptococcal Pyrogenic Exotoxin B (SpeB) Chain D 31–398（368 aa） Fragment：Streptococcal Pyrogenic Exotoxin B (SpeB)	Not recorded	ZFB (3R)-3-{[(BENZYLOXY)CARBONYL]AMINO}-2-OXO-4-PHENYLBUTANE-1-DIAZONIUM × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；293 K；Ammonium Sulphate, Glycerol, Sodium citrate, PEG 8K, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.00 Å R-free 0.288
6UKD Co-complex of S. pyogenes 10782 streptopain bound with a nitrile-based specific covalent inhibitor Deposited 2019-10-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–398（371 aa） Fragment：UNP residues 28-398	Not recorded	Q9D benzyl [(2S)-1-(3-nitrophenyl)-3-oxobutan-2-yl]carbamate × 1 NO3 NITRATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M sodium nitrate, 33% PEG3350	Resolution 1.59 Å R-free 0.189
6UQD Co-complex of S. pyogenes 10782 streptopain bound with a SuFEx-based optimized small molecule inhibitor Deposited 2019-10-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–398（371 aa） Fragment：UNP residues 28-398	Not recorded	QF4 benzyl [(1S)-2-(3-{[(4-carbamoylpiperidin-1-yl)(fluoro)oxo-lambda~6~-sulfanylidene]amino}phenyl)-1-cyanoethyl]carbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1-0.15 M sodium nitrate, 22-27% PEG3350	Resolution 2.02 Å R-free 0.257
6UQD Co-complex of S. pyogenes 10782 streptopain bound with a SuFEx-based optimized small molecule inhibitor Deposited 2019-10-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 28–398（371 aa） Fragment：UNP residues 28-398	Not recorded	QF4 benzyl [(1S)-2-(3-{[(4-carbamoylpiperidin-1-yl)(fluoro)oxo-lambda~6~-sulfanylidene]amino}phenyl)-1-cyanoethyl]carbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1-0.15 M sodium nitrate, 22-27% PEG3350	Resolution 2.02 Å R-free 0.257

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

View Construct and Data Evidence

UniProt name	SPEB_STRPY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–371； UniProt 28–398 Author chain B； PDBConstruct 1–371； UniProt 28–398 Author chain C； PDBConstruct 1–371； UniProt 28–398 Author chain D； PDBConstruct 1–371； UniProt 28–398

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	1dki
Deposition date deposition_date	1999-12-07
Structure title title	CRYSTAL STRUCTURE OF THE ZYMOGEN FORM OF STREPTOCOCCAL PYROGENIC EXOTOXIN B ACTIVE SITE (C47S) MUTANT
Keywords keywords	ZYMOGEN, CYSTEINE PROTEASE, PAPAIN-LIKE, TOXIN; TOXIN
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	37.51 Å
Radius of gyration Rg (electron density) rg_electron	37.37 Å
Forward intensity I(0) i0	311182000.00
Molecular weight molecular_weight	140420.0 kDa
Excluded volume excluded_volume	174260 Å³
Envelope volume envelope_volume	221510 Å³
Hydration-shell volume shell_volume	50700 Å³
Envelope diameter envelope_diameter	129.3 Å
Shell Rg shell_rg	42.39 Å
Envelope Rg envelope_rg	37.00 Å
Shape Rg shape_rg	37.38 Å
Total Rg total_rg	37.66 Å
Total atoms total_atoms	9923
Residues n_residues	1296
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	126.0 Å
Rg (real space) rg_real	37.60 Å
Rg uncertainty (real space) rg_real_error	1.41 Å
I(0) (real space) i0_real	3.1120e+08
I(0) uncertainty (real space) i0_real_error	5.6280e+06
Rg (reciprocal space) rg_reciprocal	37.55 Å
I(0) (reciprocal space) i0_reciprocal	311200000.0000
Solution quality estimate total_estimate	0.8786
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	42.0 Å
Skewness Skewness skewness	0.396
Kurtosis Kurtosis kurtosis	-0.367
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	74470000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.863; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.840

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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	PYROGENIC EXOTOXIN B ZYMOGEN
Molecular weight formula_weight	40318.5 kDa
Mutation mutation	C47S
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	10562

DQNFARNEKEAKDSAITFIQKSAAIKAGARSAEDIKLDKVNLGGELSGSNMYVYNISTGGFVIVSGDKRSPEILGYSTSGSFDVNGKENIASFMESYVEQIKENKKLDSTYAGTAEIKQPVVKSLLDSKGIHYNQGNPYNLLTPVIEKVKPGEQSFVGQHAATGSVATATAQIMKYHNYPNKGLKDYTYTLSSNNPYFNHPKNLFAAISTRQYNWNNILPTYSGRESNVQKMAISELMADVGISVDMDYGPSSGSAGSSRVQRALKENFGYNQSVHQINRGDFSKQDWEAQIDKELSQNQPVYYQGVGKVGGHAFVIDGADGRNFYHVNWGWGGVSDGFFRLDALNPSALGTGGGAGGFNGYQSAVVGIKP

来源 Source

来源生物 organism	Streptococcus pyogenes
NCBI Class编号 ncbi_taxonomy_id	1314
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 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	639

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1dkia_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.1 — Papain-like

Domain ID domain_id	d1dkib_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.1 — Papain-like

Domain ID domain_id	d1dkic_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.1 — Papain-like

Domain ID domain_id	d1dkid_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.1 — Papain-like

CATH v4.4 (8 domains)

Domain ID domain_id	1dkiA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	50 — Streptopain (SpeB)

Domain ID domain_id	1dkiA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	910 — Protein Binding, DinI Protein; Chain A
Homologous superfamily homologous superfamily	30 — Peptidase C10 family

Domain ID domain_id	1dkiB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	50 — Streptopain (SpeB)

Domain ID domain_id	1dkiB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	910 — Protein Binding, DinI Protein; Chain A
Homologous superfamily homologous superfamily	30 — Peptidase C10 family

Domain ID domain_id	1dkiC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	50 — Streptopain (SpeB)

Domain ID domain_id	1dkiC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	910 — Protein Binding, DinI Protein; Chain A
Homologous superfamily homologous superfamily	30 — Peptidase C10 family

Domain ID domain_id	1dkiD01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	50 — Streptopain (SpeB)

Domain ID domain_id	1dkiD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	910 — Protein Binding, DinI Protein; Chain A
Homologous superfamily homologous superfamily	30 — Peptidase C10 family

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8. Citations (1)

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Unit-cell length a length_a	46.664 Å
Unit-cell length b length_b	116.556 Å
Unit-cell length c length_c	144.726 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.17 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2180
R_work r_work	0.2180
R_free r_free	0.2450

fit	/app/data/saxs_computation/dk/1dki/1dki.fit
pddf	/app/data/pr_computation/dk/1dki/1dki.pr.out
profile	/app/data/saxs_computation/dk/1dki/1dki.dat

CRYSTAL STRUCTURE OF THE ZYMOGEN FORM OF STREPTOCOCCAL PYROGENIC EXOTOXIN B ACTIVE SITE (C47S) MUTANT

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

PYROGENIC EXOTOXIN B ZYMOGEN

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