SAXSdb — 1c4p

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

PROTEIN (STREPTOKINASE)

Streptococcus dysgalactiae subsp. equisimilis

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 149–285 Chain B； UniProt 149–285 Chain C； UniProt 149–285 Chain D； UniProt 149–285	Fragment：BETA DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.5；pH 5.5	Resolution 2.40 Å R-free 0.304

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q53284_STREQ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–137； UniProt 149–285 Author chain B； PDBConstruct 1–137； UniProt 149–285 Author chain C； PDBConstruct 1–137； UniProt 149–285 Author chain D； PDBConstruct 1–137； UniProt 149–285

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	1c4p
Deposition date deposition_date	1999-09-15
Structure title title	BETA DOMAIN OF STREPTOKINASE
Keywords keywords	PLASMINOGEN ACTIVATOR, BLOOD CLOTTING; BLOOD CLOTTING
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	26.94 Å
Radius of gyration Rg (electron density) rg_electron	26.08 Å
Forward intensity I(0) i0	62265500.00
Molecular weight molecular_weight	61617.0 kDa
Excluded volume excluded_volume	77254 Å³
Envelope volume envelope_volume	99230 Å³
Hydration-shell volume shell_volume	31900 Å³
Envelope diameter envelope_diameter	89.8 Å
Shell Rg shell_rg	33.20 Å
Envelope Rg envelope_rg	25.88 Å
Shape Rg shape_rg	26.06 Å
Total Rg total_rg	26.91 Å
Total atoms total_atoms	4350
Residues n_residues	538
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	86.9 Å
Rg (real space) rg_real	26.87 Å
Rg uncertainty (real space) rg_real_error	0.74 Å
I(0) (real space) i0_real	6.2270e+07
I(0) uncertainty (real space) i0_real_error	1.0010e+06
Rg (reciprocal space) rg_reciprocal	26.89 Å
I(0) (reciprocal space) i0_reciprocal	62270000.0000
Solution quality estimate total_estimate	0.8194
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.4 Å
Skewness Skewness skewness	0.288
Kurtosis Kurtosis kurtosis	-0.342
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8316000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.883; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1c4pa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.5 — Staphylokinase/streptokinase
Family Family family	d.15.5.1 — Staphylokinase/streptokinase

Domain ID domain_id	d1c4pb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.5 — Staphylokinase/streptokinase
Family Family family	d.15.5.1 — Staphylokinase/streptokinase

Domain ID domain_id	d1c4pc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.5 — Staphylokinase/streptokinase
Family Family family	d.15.5.1 — Staphylokinase/streptokinase

Domain ID domain_id	d1c4pd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.5 — Staphylokinase/streptokinase
Family Family family	d.15.5.1 — Staphylokinase/streptokinase

CATH v4.4 (4 domains)

Domain ID domain_id	1c4pA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	180 —

Domain ID domain_id	1c4pB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	180 —

Domain ID domain_id	1c4pC00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	180 —

Domain ID domain_id	1c4pD00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	180 —

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8. Citations (1)

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Unit-cell length a length_a	73.970 Å
Unit-cell length b length_b	83.990 Å
Unit-cell length c length_c	97.220 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	16

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2370
R_work r_work	0.2370
R_free r_free	0.3040

Description description	PROTEIN (STREPTOKINASE)
Molecular weight formula_weight	15830.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4471

BETA DOMAIN OF STREPTOKINASE

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

PROTEIN (STREPTOKINASE)

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Streptococcus dysgalactiae subsp. equisimilis
NCBI Class编号 ncbi_taxonomy_id	119602
宿主生物 host_organism	Escherichia coli BL21

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	121

fit	/app/data/saxs_computation/c4/1c4p/1c4p.fit
pddf	/app/data/pr_computation/c4/1c4p/1c4p.pr.out
profile	/app/data/saxs_computation/c4/1c4p/1c4p.dat