SAXSdb — 2oct

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

Cystatin B

Homo sapiens

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 1–98 Chain B； UniProt 1–98	Mutation：C3S, P79S	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；30 % MPD, 0.1 M HEPES, 1.4-butanediol as additive, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.40 Å R-free 0.189

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 2OCT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1STF THE REFINED 2.4 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF RECOMBINANT HUMAN STEFIN B IN COMPLEX WITH THE CYSTEINE PROTEINASE PAPAIN: A NOVEL TYPE OF PROTEINASE INHIBITOR INTERACTION Deposited 1993-04-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 1–98（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.37 Å
4N6V Partial rotational order disorder structure of human stefin B Deposited 2013-10-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain 2 8–98（91 aa） Fragment：UNP residues 8-98	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234
4N6V Partial rotational order disorder structure of human stefin B Deposited 2013-10-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 10 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain 5 8–98（91 aa） Fragment：UNP residues 8-98	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234
4N6V Partial rotational order disorder structure of human stefin B Deposited 2013-10-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain 1 8–98（91 aa） Fragment：UNP residues 8-98	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234
4N6V Partial rotational order disorder structure of human stefin B Deposited 2013-10-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain 9 8–98（91 aa） Fragment：UNP residues 8-98	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234
4N6V Partial rotational order disorder structure of human stefin B Deposited 2013-10-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain 8 8–98（91 aa） Fragment：UNP residues 8-98	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234
4N6V Partial rotational order disorder structure of human stefin B Deposited 2013-10-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain 7 8–98（91 aa） Fragment：UNP residues 8-98	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234
4N6V Partial rotational order disorder structure of human stefin B Deposited 2013-10-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain 6 8–98（91 aa） Fragment：UNP residues 8-98	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234
4N6V Partial rotational order disorder structure of human stefin B Deposited 2013-10-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain 4 8–98（91 aa） Fragment：UNP residues 8-98	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234
4N6V Partial rotational order disorder structure of human stefin B Deposited 2013-10-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain 3 8–98（91 aa） Fragment：UNP residues 8-98	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234
4N6V Partial rotational order disorder structure of human stefin B Deposited 2013-10-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain 0 8–98（91 aa） Fragment：UNP residues 8-98	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1M CAPS buffer, 0.2M Li2SO4, 2M ammonium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.234

2 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CYTB_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–98； UniProt 1–98 Author chain B； PDBConstruct 1–98； UniProt 1–98

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	2oct
Deposition date deposition_date	2006-12-21
Structure title title	Stefin B (Cystatin B) tetramer
Keywords keywords	stefin, cystatin, amyloid, domain-swapping, hand shaking, proline isomerization, PROTEIN BINDING; PROTEIN BINDING
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	19.95 Å
Radius of gyration Rg (electron density) rg_electron	19.06 Å
Forward intensity I(0) i0	8578860.00
Molecular weight molecular_weight	21817.0 kDa
Excluded volume excluded_volume	27339 Å³
Envelope volume envelope_volume	33392 Å³
Hydration-shell volume shell_volume	15103 Å³
Envelope diameter envelope_diameter	62.2 Å
Shell Rg shell_rg	24.30 Å
Envelope Rg envelope_rg	18.98 Å
Shape Rg shape_rg	19.05 Å
Total Rg total_rg	19.93 Å
Total atoms total_atoms	1550
Residues n_residues	192
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	62.3 Å
Rg (real space) rg_real	19.92 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	8.5790e+06
I(0) uncertainty (real space) i0_real_error	1.1060e+05
Rg (reciprocal space) rg_reciprocal	19.93 Å
I(0) (reciprocal space) i0_reciprocal	8579000.0000
Solution quality estimate total_estimate	0.9034
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.3 Å
Skewness Skewness skewness	0.223
Kurtosis Kurtosis kurtosis	-0.647
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2642000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.975

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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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2octa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.1 — Cystatin/monellin
Family Family family	d.17.1.2 — Cystatins

Domain ID domain_id	d2octb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.1 — Cystatin/monellin
Family Family family	d.17.1.2 — Cystatins

CATH v4.4 (2 domains)

Domain ID domain_id	2octA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2octB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	120.123 Å
Unit-cell length b length_b	30.857 Å
Unit-cell length c length_c	51.349 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.81 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1800
R_work r_work	0.1760
R_free r_free	0.1890

Description description	Cystatin B
Molecular weight formula_weight	11163.5 kDa
Mutation mutation	C3S, P79S
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	1742

Stefin B (Cystatin B) tetramer

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

Cystatin B

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) 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	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	172

fit	/app/data/saxs_computation/oc/2oct/2oct.fit
pddf	/app/data/pr_computation/oc/2oct/2oct.pr.out
profile	/app/data/saxs_computation/oc/2oct/2oct.dat