SAXSdb — 1c12

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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 heterocomplex Heteromer 蛋白 2 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: dimeric	Entity 1：PROTEIN (ANTIBODY FRAGMENT FAB) × 1 Entity 2：PROTEIN (ANTIBODY FRAGMENT FAB) × 1 缺少 UniProt 身份时不显示参考序列区间	Not recorded	TRZ TRAZEOLIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；PEG 8000, SODIUM ACETATE, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 20.0K	Resolution 2.60 Å R-free 0.270

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	1c12
Deposition date deposition_date	1999-07-20
Structure title title	INSIGHT IN ODORANT PERCEPTION: THE CRYSTAL STRUCTURE AND BINDING CHARACTERISTICS OF ANTIBODY FRAGMENTS DIRECTED AGAINST THE MUSK ODORANT TRASEOLIDE
Keywords keywords	ANTIBODY-ANTIGEN COMPLEX, SCFV FRAGMENT, CDRH3, MUSK ODORANT, ODORANT SPECIFICITY, 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	25.76 Å
Radius of gyration Rg (electron density) rg_electron	24.71 Å
Forward intensity I(0) i0	38328100.00
Molecular weight molecular_weight	47492.0 kDa
Excluded volume excluded_volume	59214 Å³
Envelope volume envelope_volume	73760 Å³
Hydration-shell volume shell_volume	25003 Å³
Envelope diameter envelope_diameter	81.4 Å
Shell Rg shell_rg	31.94 Å
Envelope Rg envelope_rg	24.33 Å
Shape Rg shape_rg	24.70 Å
Total Rg total_rg	25.58 Å
Total atoms total_atoms	3345
Residues n_residues	434
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	79.9 Å
Rg (real space) rg_real	25.73 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	3.8330e+07
I(0) uncertainty (real space) i0_real_error	5.0640e+05
Rg (reciprocal space) rg_reciprocal	25.74 Å
I(0) (reciprocal space) i0_reciprocal	38330000.0000
Solution quality estimate total_estimate	0.9119
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	28.4 Å
Skewness Skewness skewness	0.243
Kurtosis Kurtosis kurtosis	-0.579
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	6146000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.969; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.947

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	PROTEIN (ANTIBODY FRAGMENT FAB)
Molecular weight formula_weight	23391.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3459

DIELTQSPSSMSVSLGDTVSITCHASQGISSNIGWLQQKPGKSFKGLIYHGTNLEDGVPSRFSGSGSGADYSLTISSLESEDFADYYCVQYVQFPFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEA

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	PROTEIN (ANTIBODY FRAGMENT FAB)
Molecular weight formula_weight	23841.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

QVQLQESGPGLVKPSQSLSLTCTVTGYSITSDYAWNWIRQFPGNKLEWMGYISYSGSTSYSPSLKSRISLTRDTSKNQFFLQLNSVTTEDTATYYCVTSLTWLLRRKRSYWGQGTTVTVSSASTKGPSVYPLAPGSKAAASMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPE

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 non-polymer

Description description	TRAZEOLIDE
Molecular weight formula_weight	316.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	114

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7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1c12a1
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	d1c12a2
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	d1c12b1
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	d1c12b2
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	d1c12b3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	1c12A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1c12A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1c12B01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1c12B02
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	40.400 Å
Unit-cell length b length_b	84.100 Å
Unit-cell length c length_c	134.300 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	4

Space group space_group	P 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	12.000 Å
R factor r_factor	0.2050
R_work r_work	0.2050
R_free r_free	0.2700

fit	/app/data/saxs_computation/c1/1c12/1c12.fit
pddf	/app/data/pr_computation/c1/1c12/1c12.pr.out
profile	/app/data/saxs_computation/c1/1c12/1c12.dat

INSIGHT IN ODORANT PERCEPTION: THE CRYSTAL STRUCTURE AND BINDING CHARACTERISTICS OF ANTIBODY FRAGMENTS DIRECTED AGAINST THE MUSK ODORANT TRASEOLIDE

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

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)