SAXSdb — 1cd0

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

PROTEIN (JTO, A VARIABLE DOMAIN FROM LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN)

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–111 Chain B； UniProt 1–111	Fragment：IMMUNOGLOBULIN VARIABLE DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；27.5% PEG6000, 0.08 M SODIUM CACODYLATE PH 6.5, 0.1 M SODIUM ACETATE	Resolution 1.90 Å R-free 0.240

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 1CD0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1PEW High Resolution Crystal Structure of Jto2, a mutant of the non-amyloidogenic Lamba6 Light Chain, Jto Deposited 2003-05-22	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 2–111（110 aa） Fragment：IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN Chain B 2–111（110 aa） Fragment：IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN	Mutation：D29A Mutation：D29A	CD CADMIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；0.1M Na Acetate, 0.8M Amm. Sulfate, 100mM Cadmium chloride, 10% n-Decyl-B-D-maltoside, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.273
1PEW High Resolution Crystal Structure of Jto2, a mutant of the non-amyloidogenic Lamba6 Light Chain, Jto Deposited 2003-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–111（110 aa） Fragment：IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN Chain B 2–111（110 aa） Fragment：IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN	Mutation：D29A Mutation：D29A	CD CADMIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；0.1M Na Acetate, 0.8M Amm. Sulfate, 100mM Cadmium chloride, 10% n-Decyl-B-D-maltoside, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.273
1PEW High Resolution Crystal Structure of Jto2, a mutant of the non-amyloidogenic Lamba6 Light Chain, Jto Deposited 2003-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–111（110 aa） Fragment：IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN Chain B 2–111（110 aa） Fragment：IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN	Mutation：D29A Mutation：D29A	CD CADMIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；0.1M Na Acetate, 0.8M Amm. Sulfate, 100mM Cadmium chloride, 10% n-Decyl-B-D-maltoside, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.273

1 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LV6C_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–111； UniProt 1–111 Author chain B； PDBConstruct 1–111； UniProt 1–111

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	1cd0
Deposition date deposition_date	1999-03-05
Structure title title	STRUCTURE OF HUMAN LAMDA-6 LIGHT CHAIN DIMER JTO
Keywords keywords	IMMUNOGLOBULIN, BENCE-JONES PROTEIN, LAMDA-6, IMMUNE SYSTEM; IMMUNE SYSTEM
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	18.35 Å
Radius of gyration Rg (electron density) rg_electron	17.26 Å
Forward intensity I(0) i0	11703600.00
Molecular weight molecular_weight	23729.0 kDa
Excluded volume excluded_volume	28917 Å³
Envelope volume envelope_volume	33498 Å³
Hydration-shell volume shell_volume	16498 Å³
Envelope diameter envelope_diameter	58.8 Å
Shell Rg shell_rg	23.08 Å
Envelope Rg envelope_rg	17.42 Å
Shape Rg shape_rg	17.21 Å
Total Rg total_rg	18.25 Å
Total atoms total_atoms	1670
Residues n_residues	221
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	57.8 Å
Rg (real space) rg_real	18.26 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	1.1700e+07
I(0) uncertainty (real space) i0_real_error	1.3190e+05
Rg (reciprocal space) rg_reciprocal	18.28 Å
I(0) (reciprocal space) i0_reciprocal	11700000.0000
Solution quality estimate total_estimate	0.9022
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.2 Å
Skewness Skewness skewness	0.180
Kurtosis Kurtosis kurtosis	-0.444
Angular range angular_range	— – 0.4350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3977000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 1.000

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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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1cd0a_
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	d1cd0b_
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 (2 domains)

Domain ID domain_id	1cd0A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1cd0B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	42.900 Å
Unit-cell length b length_b	60.500 Å
Unit-cell length c length_c	73.400 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	1.900 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.1840
R_free r_free	0.2400

Description description	PROTEIN (JTO, A VARIABLE DOMAIN FROM LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN)
Molecular weight formula_weight	12097.1 kDa
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	1917

STRUCTURE OF HUMAN LAMDA-6 LIGHT CHAIN DIMER JTO

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

PROTEIN (JTO, A VARIABLE DOMAIN FROM LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN)

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	247

fit	/app/data/saxs_computation/cd/1cd0/1cd0.fit
pddf	/app/data/pr_computation/cd/1cd0/1cd0.pr.out
profile	/app/data/saxs_computation/cd/1cd0/1cd0.dat