SAXSdb — 1b0w

▼

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

BENCE-JONES KAPPA I PROTEIN BRE

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–108	Fragment：VARIABLE DOMAIN OF LIGHT CHAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；CRYSTALS OF BRE (20MG/ML IN 0.1M TRIS BUFFER, PH 7) WERE GROWN AT RT IN HANGING-DROPS USING 2.5M AMMONIUM SULFATE IN 0.1M CITRATE BUFFER (PH 5.5)., pH 6.5, VAPOR DIFFUSION, HANGING DROP	Resolution 1.80 Å R-free 0.299
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–108	Fragment：VARIABLE DOMAIN OF LIGHT CHAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；CRYSTALS OF BRE (20MG/ML IN 0.1M TRIS BUFFER, PH 7) WERE GROWN AT RT IN HANGING-DROPS USING 2.5M AMMONIUM SULFATE IN 0.1M CITRATE BUFFER (PH 5.5)., pH 6.5, VAPOR DIFFUSION, HANGING DROP	Resolution 1.80 Å R-free 0.299
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1–108	Fragment：VARIABLE DOMAIN OF LIGHT CHAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；CRYSTALS OF BRE (20MG/ML IN 0.1M TRIS BUFFER, PH 7) WERE GROWN AT RT IN HANGING-DROPS USING 2.5M AMMONIUM SULFATE IN 0.1M CITRATE BUFFER (PH 5.5)., pH 6.5, VAPOR DIFFUSION, HANGING DROP	Resolution 1.80 Å R-free 0.299

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 1B0W	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1JV5 Anti-blood group A Fv Deposited 2001-08-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 15–121（107 aa） Fragment：anti-blood group A Fv	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；300 K；PEG 4000, HEPES, Calcium Chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.20 Å R-free 0.223
2Q20 Structure of the germline Vk1 O18/O8 light chain variable domain homodimer Deposited 2007-05-25	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–107（107 aa） Chain B 1–107（107 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；Protein: 890 micromolar in 10 mM TRIS pH 7.4. Mother Liquor: 15-30% (w/v) PEG 4K, 0.2 Li2SO4, 0.1 M TRIS pH 7.9-8.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.30 Å R-free 0.148
7CZQ S protein of SARS-CoV-2 in complex bound with P2B-1A10 Deposited 2020-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric	Chain K 23–117（95 aa） Chain N 23–117（95 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
7CZU S protein of SARS-CoV-2 in complex bound with P5A-1B6_2B Deposited 2020-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric	Chain K 23–117（95 aa） Chain N 23–117（95 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7CZV S protein of SARS-CoV-2 in complex bound with P5A-1B6_3B Deposited 2020-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric	Chain K 23–117（95 aa） Chain M 23–117（95 aa） Chain N 23–117（95 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

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

View Construct and Data Evidence

UniProt name	KV1B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–108； UniProt 1–108 Author chain B； PDBConstruct 1–108； UniProt 1–108 Author chain C； PDBConstruct 1–108； UniProt 1–108

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1b0w
Deposition date deposition_date	1998-11-13
Structure title title	Structural comparison of amyloidogenic light chain dimer in two crystal forms with nonamyloidogenic counterparts
Keywords keywords	IMMUNOGLOBULIN, AMYLOID, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	35.49 Å
Radius of gyration Rg (electron density) rg_electron	35.54 Å
Forward intensity I(0) i0	21492500.00
Molecular weight molecular_weight	35800.0 kDa
Excluded volume excluded_volume	44496 Å³
Envelope volume envelope_volume	67517 Å³
Hydration-shell volume shell_volume	18312 Å³
Envelope diameter envelope_diameter	112.5 Å
Shell Rg shell_rg	36.35 Å
Envelope Rg envelope_rg	33.83 Å
Shape Rg shape_rg	35.57 Å
Total Rg total_rg	35.53 Å
Total atoms total_atoms	2520
Residues n_residues	324
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	107.3 Å
Rg (real space) rg_real	35.86 Å
Rg uncertainty (real space) rg_real_error	0.79 Å
I(0) (real space) i0_real	2.1490e+07
I(0) uncertainty (real space) i0_real_error	3.3710e+05
Rg (reciprocal space) rg_reciprocal	35.64 Å
I(0) (reciprocal space) i0_reciprocal	21490000.0000
Solution quality estimate total_estimate	0.5848
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	47.7 Å
Skewness Skewness skewness	0.313
Kurtosis Kurtosis kurtosis	-0.790
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	776200.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.115; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.252; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1b0wa_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1b0wb_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1b0wc_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

CATH v4.4 (3 domains)

Domain ID domain_id	1b0wA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1b0wB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1b0wC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

8. Citations (2)

▶

Unit-cell length a length_a	82.040 Å
Unit-cell length b length_b	142.110 Å
Unit-cell length c length_c	77.860 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	24

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	5.000 Å
R factor r_factor	—
R_work r_work	0.2260
R_free r_free	0.2990

Description description	BENCE-JONES KAPPA I PROTEIN BRE
Molecular weight formula_weight	11945.1 kDa
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	2624

Structural comparison of amyloidogenic light chain dimer in two crystal forms with nonamyloidogenic counterparts

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

BENCE-JONES KAPPA I PROTEIN BRE

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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

8. Citations (2)

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	104

fit	/app/data/saxs_computation/b0/1b0w/1b0w.fit
pddf	/app/data/pr_computation/b0/1b0w/1b0w.pr.out
profile	/app/data/saxs_computation/b0/1b0w/1b0w.dat