SAXSdb — 1cbv

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

No usable UniProt protein identity is available for this entry.

七张关系表仍保留该条目的 assembly 与组成信息，但缺少统一蛋白身份时，不能可靠建立跨 PDB 的同蛋白Chain接。

Assembly Composition of the Current Entry

Assembly	Oligomeric State	实体与Construct证据	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Heteromer 蛋白 2 / DNA 1 / RNA 0 / 其他Polymer 0 PDB declaration: trimeric	Entity 1：;DNA (5'-D(TPTP*T)-3') ; × 1 Entity 2：PROTEIN (FAB (BV04-01) AUTOANTIBODY-LIGHT CHAIN) × 1 Entity 3：PROTEIN (FAB (BV04-01) AUTOANTIBODY-HEAVY CHAIN) × 1 缺少 UniProt 身份时不显示参考序列区间	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.66 Å

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	1cbv
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	PROTEIN-DNA COMPLEX, SINGLE STRAND, IMMUNE SYSTEM-DNA COMPLEX; IMMUNE SYSTEM/DNA
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	26.50 Å
Radius of gyration Rg (electron density) rg_electron	25.26 Å
Forward intensity I(0) i0	41857600.00
Molecular weight molecular_weight	48554.0 kDa
Excluded volume excluded_volume	60019 Å³
Envelope volume envelope_volume	75066 Å³
Hydration-shell volume shell_volume	24981 Å³
Envelope diameter envelope_diameter	83.5 Å
Shell Rg shell_rg	32.43 Å
Envelope Rg envelope_rg	24.86 Å
Shape Rg shape_rg	25.24 Å
Total Rg total_rg	26.12 Å
Total atoms total_atoms	3408
Residues n_residues	441
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	81.4 Å
Rg (real space) rg_real	26.50 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	4.1860e+07
I(0) uncertainty (real space) i0_real_error	6.3740e+05
Rg (reciprocal space) rg_reciprocal	26.50 Å
I(0) (reciprocal space) i0_reciprocal	41860000.0000
Solution quality estimate total_estimate	0.9075
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.1 Å
Skewness Skewness skewness	0.262
Kurtosis Kurtosis kurtosis	-0.627
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5528000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.975; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.896

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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	;DNA (5'-D(TPTP*T)-3') ;
Molecular weight formula_weight	867.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D
Atom count atom_count	3408

TTT

Entity 2 Entity 2 polymer

Description description	PROTEIN (FAB (BV04-01) AUTOANTIBODY-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

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 3 Entity 3 polymer

Description description	PROTEIN (FAB (BV04-01) AUTOANTIBODY-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	d1cbvh1
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	d1cbvh2
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	d1cbvl1
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	d1cbvl2
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	1cbvH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1cbvH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1cbvL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1cbvL02
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	63.500 Å
Unit-cell length b length_b	99.200 Å
Unit-cell length c length_c	36.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.30 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.660 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.1910
R_work r_work	0.1910
R_free r_free	—

fit	/app/data/saxs_computation/cb/1cbv/1cbv.fit
pddf	/app/data/pr_computation/cb/1cbv/1cbv.pr.out
profile	/app/data/saxs_computation/cb/1cbv/1cbv.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

Assembly Composition of the Current Entry

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 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)