SAXSdb — 1cv8

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

STAPHOPAIN

OrganismNot specified

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 1–174	Not recorded	ACT ACETATE ION × 2 E64 N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；5 M AMMONIUM ACETATE, 2MM DTT, 5MM E-64, 50 MM MES/TRIS BUFFER PH 6.0 5MM E-64	Resolution 1.75 Å R-free 0.239

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	SSPP_STAAU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–174； UniProt 1–174

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	1cv8
Deposition date deposition_date	1998-05-08
Structure title title	STAPHOPAIN, CYSTEINE PROTEINASE FROM STAPHYLOCOCCUS AUREUS V8
Keywords keywords	CYSTEINE PROTEASE, THIOL PROTEASE, PAPAIN FAMILY; CYSTEINE PROTEASE
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	17.09 Å
Radius of gyration Rg (electron density) rg_electron	15.76 Å
Forward intensity I(0) i0	8176550.00
Molecular weight molecular_weight	20110.0 kDa
Excluded volume excluded_volume	24779 Å³
Envelope volume envelope_volume	28165 Å³
Hydration-shell volume shell_volume	15062 Å³
Envelope diameter envelope_diameter	57.4 Å
Shell Rg shell_rg	21.72 Å
Envelope Rg envelope_rg	16.17 Å
Shape Rg shape_rg	15.76 Å
Total Rg total_rg	16.76 Å
Total atoms total_atoms	1416
Residues n_residues	173
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	58.1 Å
Rg (real space) rg_real	17.01 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	8.1770e+06
I(0) uncertainty (real space) i0_real_error	8.5490e+04
Rg (reciprocal space) rg_reciprocal	17.02 Å
I(0) (reciprocal space) i0_reciprocal	8177000.0000
Solution quality estimate total_estimate	0.8629
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.2 Å
Skewness Skewness skewness	0.230
Kurtosis Kurtosis kurtosis	-0.210
Angular range angular_range	— – 0.4650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1989000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.752; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.958

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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	STAPHOPAIN
Molecular weight formula_weight	19870.1 kDa
EC 编号 ec_number	3.4.22.-
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1539

YNEQYVNKLENFKIRETQGNNGWCAGYTMSALLNATYNTNKYHAEAVMRFLHPNLQGQQFQFTGLTPREMIYFGQTQGRSPQLLNRMTTYNEVDNLTKNNKGIAILGSRVESRNGMHAGHAMAVVGNAKLNNGQEVIIIWNPWDNGFMTQDAKNNVIPVSNGDHYQWYSSIYGY

Entity 2 Entity 2 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE
Molecular weight formula_weight	360.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	123

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1cv8a_
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 (1 domains)

Domain ID domain_id	1cv8A00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

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8. Citations (1)

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Unit-cell length a length_a	61.139 Å
Unit-cell length b length_b	61.139 Å
Unit-cell length c length_c	195.063 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	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1830
R_work r_work	0.2000
R_free r_free	0.2390

fit	/app/data/saxs_computation/cv/1cv8/1cv8.fit
pddf	/app/data/pr_computation/cv/1cv8/1cv8.pr.out
profile	/app/data/saxs_computation/cv/1cv8/1cv8.dat

STAPHOPAIN, CYSTEINE PROTEINASE FROM STAPHYLOCOCCUS AUREUS V8

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

STAPHOPAIN

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