SAXSdb — 3kg5

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

B-cell antigen receptor complex-associated protein beta 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 26–159 Chain B； UniProt 26–159	Fragment：extracellular domain	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 4；298 K；0.6M Na formate, 100mM Na Acetate, pH 4.0, VAPOR DIFFUSION, temperature 298K	Resolution 3.20 Å R-free 0.263
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 26–159	Fragment：extracellular domain	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 4；298 K；0.6M Na formate, 100mM Na Acetate, pH 4.0, VAPOR DIFFUSION, temperature 298K	Resolution 3.20 Å R-free 0.263
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 26–159	Fragment：extracellular domain	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 4；298 K；0.6M Na formate, 100mM Na Acetate, pH 4.0, VAPOR DIFFUSION, temperature 298K	Resolution 3.20 Å R-free 0.263

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 3KG5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7WSO Structure of a membrane protein G Deposited 2022-01-30	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 44–182（139 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.03 Å
7WSP Structure of a membrane protein M Deposited 2022-01-30	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 44–182（139 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 4.09 Å
7XQ8 Structure of human B-cell antigen receptor of the IgM isotype Deposited 2022-05-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 1–229（229 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7XT6 Structure of a membrane protein M3 Deposited 2022-05-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 44–182（139 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.63 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CD79B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–134； UniProt 26–159 Author chain B； PDBConstruct 1–134； UniProt 26–159

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	3kg5
Deposition date deposition_date	2009-10-28
Structure title title	Crystal structure of human Ig-beta homodimer
Keywords keywords	CD79b, Ig-beta, BCR, Immunoglobulin domain, 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	19.27 Å
Radius of gyration Rg (electron density) rg_electron	18.46 Å
Forward intensity I(0) i0	11705600.00
Molecular weight molecular_weight	24019.0 kDa
Excluded volume excluded_volume	29466 Å³
Envelope volume envelope_volume	36261 Å³
Hydration-shell volume shell_volume	16848 Å³
Envelope diameter envelope_diameter	64.9 Å
Shell Rg shell_rg	23.78 Å
Envelope Rg envelope_rg	18.59 Å
Shape Rg shape_rg	18.46 Å
Total Rg total_rg	19.28 Å
Total atoms total_atoms	1676
Residues n_residues	206
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	62.2 Å
Rg (real space) rg_real	19.19 Å
Rg uncertainty (real space) rg_real_error	0.29 Å
I(0) (real space) i0_real	1.1710e+07
I(0) uncertainty (real space) i0_real_error	1.4620e+05
Rg (reciprocal space) rg_reciprocal	19.20 Å
I(0) (reciprocal space) i0_reciprocal	11710000.0000
Solution quality estimate total_estimate	0.9012
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	0.195
Kurtosis Kurtosis kurtosis	-0.499
Angular range angular_range	— – 0.4150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2515000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.984

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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) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3kg5A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3kg5B00
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	129.800 Å
Unit-cell length b length_b	129.800 Å
Unit-cell length c length_c	129.800 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	48

Space group space_group	P 41 3 2
Space-group number int_tables_number	213
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	46.000 Å
R factor r_factor	—
R_work r_work	0.1810
R_free r_free	0.2630

Description description	B-cell antigen receptor complex-associated protein beta chain
Molecular weight formula_weight	15499.6 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	1678

Crystal structure of human Ig-beta homodimer

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

B-cell antigen receptor complex-associated protein beta 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) 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	2

fit	/app/data/saxs_computation/kg/3kg5/3kg5.fit
pddf	/app/data/pr_computation/kg/3kg5/3kg5.pr.out
profile	/app/data/saxs_computation/kg/3kg5/3kg5.dat