SAXSdb — 1c79

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

STAPHYLOKINASE

Staphylococcus aureus

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 28–163 Chain B； UniProt 28–163	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；PEG 1000, pH 8.5, vapor diffusion/hanging drop, temperature 293K	Resolution 2.30 Å R-free 0.267

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 1C79	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C76 STAPHYLOKINASE (SAK) MONOMER Deposited 2000-02-01	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 28–163（136 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；PEG 8000, pH 8.0, vapor diffusion/hanging drop, temperature 293K	Resolution 2.25 Å R-free 0.273
1C77 STAPHYLOKINASE (SAK) DIMER Deposited 2000-02-01	Parsed fields agree	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 28–163（136 aa） Chain B 28–163（136 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；PEG 1000, pH 8.5, vapor diffusion/hanging drop, temperature 293K	Resolution 2.30 Å R-free 0.267
1C78 STAPHYLOKINASE (SAK) DIMER Deposited 2000-02-01	Parsed fields agree	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 28–163（136 aa） Chain B 28–163（136 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；PEG 1000, pH 8.5, vapor diffusion/hanging drop, temperature 293K	Resolution 2.30 Å R-free 0.267
1SSN STAPHYLOKINASE, SAKSTAR VARIANT, NMR, 20 STRUCTURES Deposited 1998-06-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–163（136 aa）	Mutation：SAKSTAR VARIANT	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.7；300 K NMR sample composition WATER	Resolution not provided
2SAK STAPHYLOKINASE (SAKSTAR VARIANT) Deposited 1997-02-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 43–163（121 aa）	Mutation：SAKSTAR VARIANT	TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；PROTEIN WAS CRYSTALLIZED FROM 0.2M MGCL2, O.1M TRIS BUFFER PH 8.5 AND 30 % PEG 4K, USING MICROSEEDING TECHNIQUES.	Resolution 1.80 Å R-free 0.237

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SAK_STAAU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–136； UniProt 28–163 Author chain B； PDBConstruct 1–136； UniProt 28–163

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	1c79
Deposition date deposition_date	2000-02-01
Structure title title	STAPHYLOKINASE (SAK) DIMER
Keywords keywords	BETA-GRASP FAMILY, 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	21.51 Å
Radius of gyration Rg (electron density) rg_electron	20.45 Å
Forward intensity I(0) i0	13457100.00
Molecular weight molecular_weight	29421.0 kDa
Excluded volume excluded_volume	37653 Å³
Envelope volume envelope_volume	49441 Å³
Hydration-shell volume shell_volume	20155 Å³
Envelope diameter envelope_diameter	71.2 Å
Shell Rg shell_rg	26.75 Å
Envelope Rg envelope_rg	20.31 Å
Shape Rg shape_rg	20.44 Å
Total Rg total_rg	21.45 Å
Total atoms total_atoms	2084
Residues n_residues	258
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	68.4 Å
Rg (real space) rg_real	21.36 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	1.3460e+07
I(0) uncertainty (real space) i0_real_error	1.6900e+05
Rg (reciprocal space) rg_reciprocal	21.39 Å
I(0) (reciprocal space) i0_reciprocal	13460000.0000
Solution quality estimate total_estimate	0.8949
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.2 Å
Skewness Skewness skewness	0.071
Kurtosis Kurtosis kurtosis	-0.555
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3215000.0000
Real-space data points n_real_points	69
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: 0.982

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1c79a_
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	d1c79b_
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 (2 domains)

Domain ID domain_id	1c79A00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	1c79B00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	130 —

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8. Citations (1)

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Unit-cell length a length_a	43.870 Å
Unit-cell length b length_b	59.260 Å
Unit-cell length c length_c	102.420 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2040
R_work r_work	0.1980
R_free r_free	0.2670

Description description	STAPHYLOKINASE
Molecular weight formula_weight	15487.6 kDa
EC 编号 ec_number	3.4.24.29
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2084

STAPHYLOKINASE (SAK) DIMER

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

STAPHYLOKINASE

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Staphylococcus aureus
NCBI Class编号 ncbi_taxonomy_id	1280
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/c7/1c79/1c79.fit
pddf	/app/data/pr_computation/c7/1c79/1c79.pr.out
profile	/app/data/saxs_computation/c7/1c79/1c79.dat