SAXSdb — 1nbv

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

IGG2B-KAPPA BV04-01 FAB (HEAVY CHAIN)

Mus musculus

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain H； UniProt 1–98	Not recorded	IGG2B-KAPPA BV04-01 FAB (LIGHT CHAIN) × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.00 Å

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 1NBV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CIC IDIOTOPE-ANTI-IDIOTOPE FAB-FAB COMPLEX; D1.3-E225 Deposited 1999-03-31	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–217（217 aa） Fragment：FAB IMMUNOGLOBULIN FRAGMENT	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.9；12% PEG 800, 75 MILLIMOLAR SODIUM ACETATE PH 4.85 10MGM/ML PROTEIN CONCENTRATION , pH 4.9	Resolution 2.50 Å
1HQ4 STRUCTURE OF NATIVE CATALYTIC ANTIBODY HA5-19A4 Deposited 2000-12-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–99（99 aa） Fragment：VARIABLE REGIONS OF FAB LIGHT AND HEAVY CHAINS	Not recorded	CD CADMIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；PEG 6000, cadmium chloride, hepes, ph 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.265
1HQ4 STRUCTURE OF NATIVE CATALYTIC ANTIBODY HA5-19A4 Deposited 2000-12-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–99（99 aa） Fragment：VARIABLE REGIONS OF FAB LIGHT AND HEAVY CHAINS	Not recorded	CD CADMIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；PEG 6000, cadmium chloride, hepes, ph 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.265
1MAM CRYSTAL STRUCTURE TO 2.45 A RESOLUTION OF A MONOCLONAL FAB SPECIFIC FOR THE BRUCELLA A CELL WALL POLYSACCHARIDE ANTIGEN Deposited 1992-01-14	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–98（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.45 Å
1OSP CRYSTAL STRUCTURE OF OUTER SURFACE PROTEIN A OF BORRELIA BURGDORFERI COMPLEXED WITH A MURINE MONOCLONAL ANTIBODY FAB Deposited 1996-11-23	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 1–98（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.95 Å R-free 0.295
2RGS FC-fragment of monoclonal antibody IGG2B from Mus musculus Deposited 2007-10-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 117–334（218 aa） Fragment：Fc-fragment Chain B 117–334（218 aa） Fragment：Fc-fragment	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；301 K；20% PEG2000, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 301K	Resolution 2.13 Å R-free 0.213
5UBX Crystal structure of a mutant mIgG2b Fc heterodimer in complex with Protein A peptide analog Z34C Deposited 2016-12-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 108–335（228 aa） Fragment：UNP residues 108-335 Chain B 108–335（228 aa） Fragment：UNP residues 108-335	Mutation：P307T, Q309L, V370K, K409R Mutation：I253D, F405L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；17% PEG 3350, 0.2 M LiCl, 0.1 M Tris, pH 8.0	Resolution 2.70 Å R-free 0.257
6KRU Crystal structure of mouse IgG2b Fc Deposited 2019-08-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 117–334（218 aa） Chain B 117–334（218 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；16% PEG3350, 0.2 M lithium chloride, and 0.1 M Bis-Tris (pH 6.5)	Resolution 2.30 Å R-free 0.237
6KRU Crystal structure of mouse IgG2b Fc Deposited 2019-08-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 117–334（218 aa） Chain D 117–334（218 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；16% PEG3350, 0.2 M lithium chloride, and 0.1 M Bis-Tris (pH 6.5)	Resolution 2.30 Å R-free 0.237
6KRU Crystal structure of mouse IgG2b Fc Deposited 2019-08-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 117–334（218 aa） Chain F 117–334（218 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；16% PEG3350, 0.2 M lithium chloride, and 0.1 M Bis-Tris (pH 6.5)	Resolution 2.30 Å R-free 0.237
6KRV Crystal structure of mouse IgG2b Fc complexed with B domain of Protein A Deposited 2019-08-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 117–334（218 aa） Chain B 117–334（218 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；60% (v/v) Tacsimate (pH 7.0)	Resolution 3.30 Å R-free 0.250
6KRV Crystal structure of mouse IgG2b Fc complexed with B domain of Protein A Deposited 2019-08-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 117–334（218 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；60% (v/v) Tacsimate (pH 7.0)	Resolution 3.30 Å R-free 0.250

8 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GCBM_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain H； PDBConstruct 122–219； 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	1nbv
Deposition date deposition_date	1993-03-16
Structure title title	AN AUTOANTIBODY TO SINGLE-STRANDED DNA: COMPARISON OF THE THREE-DIMENSIONAL STRUCTURES OF THE UNLIGANDED FAB AND A DEOXYNUCLEOTIDE-FAB COMPLEX
Keywords keywords	IMMUNOGLOBULIN; IMMUNOGLOBULIN
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	26.17 Å
Radius of gyration Rg (electron density) rg_electron	25.00 Å
Forward intensity I(0) i0	39561200.00
Molecular weight molecular_weight	47621.0 kDa
Excluded volume excluded_volume	59071 Å³
Envelope volume envelope_volume	73372 Å³
Hydration-shell volume shell_volume	24628 Å³
Envelope diameter envelope_diameter	83.7 Å
Shell Rg shell_rg	32.10 Å
Envelope Rg envelope_rg	24.66 Å
Shape Rg shape_rg	24.98 Å
Total Rg total_rg	25.84 Å
Total atoms total_atoms	3347
Residues n_residues	438
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	81.2 Å
Rg (real space) rg_real	26.16 Å
Rg uncertainty (real space) rg_real_error	0.60 Å
I(0) (real space) i0_real	3.9560e+07
I(0) uncertainty (real space) i0_real_error	6.0780e+05
Rg (reciprocal space) rg_reciprocal	26.17 Å
I(0) (reciprocal space) i0_reciprocal	39560000.0000
Solution quality estimate total_estimate	0.9115
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.9 Å
Skewness Skewness skewness	0.253
Kurtosis Kurtosis kurtosis	-0.605
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5774000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.971; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.951

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	IGG2B-KAPPA BV04-01 FAB (LIGHT CHAIN)
Molecular weight formula_weight	24109.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L
Atom count atom_count	3347

DVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090

Entity 2 Entity 2 polymer

Description description	IGG2B-KAPPA BV04-01 FAB (HEAVY CHAIN)
Molecular weight formula_weight	23553.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

EVQPVETGGGLVQPKGSLKLSCAASGFSFNTNAMNWVRQAPGKGLEWVARIRSKSNNYATYYADSVKDRFTISRDDSQNMLYLQMNNLKTEDTAMYYCVRDQTGTAWFAYWGQGTLVTVSAAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLE

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1nbvh1
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	d1nbvh2
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.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d1nbvl1
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	d1nbvl2
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.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (4 domains)

Domain ID domain_id	1nbvH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1nbvH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1nbvL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1nbvL02
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 (2)

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Unit-cell length a length_a	58.400 Å
Unit-cell length b length_b	43.700 Å
Unit-cell length c length_c	41.500 Å
Unit-cell angle α angle_alpha	83.40 °
Unit-cell angle β angle_beta	89.40 °
Unit-cell angle γ angle_gamma	84.40 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.2460
R_work r_work	0.2460
R_free r_free	—

fit	/app/data/saxs_computation/nb/1nbv/1nbv.fit
pddf	/app/data/pr_computation/nb/1nbv/1nbv.pr.out
profile	/app/data/saxs_computation/nb/1nbv/1nbv.dat

AN AUTOANTIBODY TO SINGLE-STRANDED DNA: COMPARISON OF THE THREE-DIMENSIONAL STRUCTURES OF THE UNLIGANDED FAB AND A DEOXYNUCLEOTIDE-FAB COMPLEX

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

IGG2B-KAPPA BV04-01 FAB (HEAVY 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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)