SAXSdb — 1pew

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

Jto2, a LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN

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 2–111 Chain B； UniProt 2–111	Fragment：IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN 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
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 2–111 Chain B； UniProt 2–111	Fragment：IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN 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
3	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 2–111 Chain B； UniProt 2–111	Fragment：IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN 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

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 1PEW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CD0 STRUCTURE OF HUMAN LAMDA-6 LIGHT CHAIN DIMER JTO Deposited 1999-03-05	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 1–111（111 aa） Fragment：IMMUNOGLOBULIN VARIABLE DOMAIN Chain B 1–111（111 aa） Fragment：IMMUNOGLOBULIN VARIABLE DOMAIN	Not recorded	No recorded non-water small molecule	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

1 other PDB entries and 1 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 2–109； UniProt 2–111 Author chain B； PDBConstruct 2–109； UniProt 2–111

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	1pew
Deposition date deposition_date	2003-05-22
Structure title title	High Resolution Crystal Structure of Jto2, a mutant of the non-amyloidogenic Lamba6 Light Chain, Jto
Keywords keywords	Beta Sheet, 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	20.45 Å
Radius of gyration Rg (electron density) rg_electron	19.73 Å
Forward intensity I(0) i0	12087700.00
Molecular weight molecular_weight	23867.0 kDa
Excluded volume excluded_volume	28773 Å³
Envelope volume envelope_volume	34833 Å³
Hydration-shell volume shell_volume	15493 Å³
Envelope diameter envelope_diameter	67.4 Å
Shell Rg shell_rg	24.86 Å
Envelope Rg envelope_rg	19.93 Å
Shape Rg shape_rg	19.72 Å
Total Rg total_rg	20.44 Å
Total atoms total_atoms	1651
Residues n_residues	208
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	67.9 Å
Rg (real space) rg_real	20.49 Å
Rg uncertainty (real space) rg_real_error	0.43 Å
I(0) (real space) i0_real	1.2090e+07
I(0) uncertainty (real space) i0_real_error	1.5480e+05
Rg (reciprocal space) rg_reciprocal	20.49 Å
I(0) (reciprocal space) i0_reciprocal	12090000.0000
Solution quality estimate total_estimate	0.8894
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.4 Å
Skewness Skewness skewness	0.367
Kurtosis Kurtosis kurtosis	-0.440
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2238000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.872; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.948; Smooth: 0.995

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Jto2, a LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN
Molecular weight formula_weight	11899.0 kDa
Mutation mutation	D29A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1755

NFMLNQPHSVSESPGKTVTISCTRSSGNIASNYVQWYQQRSAPITVIYEDNQRPSGVPDRFAGSIDRSSNSASLTISGLKTEDEADYYCQSYDARNVVFGGGTRLTVLG

来源 Source

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	104

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1pewa_
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	d1pewb_
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	1pewA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1pewB00
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	73.577 Å
Unit-cell length b length_b	73.577 Å
Unit-cell length c length_c	92.298 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	16

Space group space_group	P 41 2 2
Space-group number int_tables_number	91
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2533
R_work r_work	0.2522
R_free r_free	0.2729

fit	/app/data/saxs_computation/pe/1pew/1pew.fit
pddf	/app/data/pr_computation/pe/1pew/1pew.pr.out
profile	/app/data/saxs_computation/pe/1pew/1pew.dat

High Resolution Crystal Structure of Jto2, a mutant of the non-amyloidogenic Lamba6 Light Chain, Jto

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

Jto2, a LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN

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