SAXSdb — 1dlf

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

ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S)

OrganismNot specified

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 L； UniProt 1–113	Fragment：FV FRAGMENT (VH AND VL DOMAINS)	ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S) × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.25；pH 5.25	Resolution 1.45 Å R-free 0.230

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q9JL82_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain L； PDBConstruct 1–113； UniProt 1–113

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	1dlf
Deposition date deposition_date	1998-07-14
Structure title title	HIGH RESOLUTION CRYSTAL STRUCTURE OF THE FV FRAGMENT FROM AN ANTI-DANSYL SWITCH VARIANT ANTIBODY IGG2A(S) CRYSTALLIZED AT PH 5.25
Keywords keywords	FV FRAGMENT, 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	19.17 Å
Radius of gyration Rg (electron density) rg_electron	17.95 Å
Forward intensity I(0) i0	13201400.00
Molecular weight molecular_weight	26428.0 kDa
Excluded volume excluded_volume	32691 Å³
Envelope volume envelope_volume	37075 Å³
Hydration-shell volume shell_volume	17495 Å³
Envelope diameter envelope_diameter	65.0 Å
Shell Rg shell_rg	23.89 Å
Envelope Rg envelope_rg	18.22 Å
Shape Rg shape_rg	17.87 Å
Total Rg total_rg	19.03 Å
Total atoms total_atoms	1857
Residues n_residues	233
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	64.2 Å
Rg (real space) rg_real	19.09 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	1.3200e+07
I(0) uncertainty (real space) i0_real_error	1.5480e+05
Rg (reciprocal space) rg_reciprocal	19.10 Å
I(0) (reciprocal space) i0_reciprocal	13200000.0000
Solution quality estimate total_estimate	0.8857
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.2 Å
Skewness Skewness skewness	0.226
Kurtosis Kurtosis kurtosis	-0.404
Angular range angular_range	— – 0.4150 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	3481000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.998

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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	ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S)
Molecular weight formula_weight	12386.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L
Atom count atom_count	2394

DVVMTQTPLSLPVSLGNQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPFTFGSGTKLEIKR

Entity 2 Entity 2 polymer

Description description	ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S)
Molecular weight formula_weight	14152.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

EVKLEESGGGLVQPGGSMKLSCATSGFTFSDAWMDWVRQSPEKGLEWVAEIRNKANNHATYYAESVKGRFTISRDDSKRRVYLQMNTLRAEDTGIYYCTGIYYHYPWFAYWGQGTLVTVSAEPR

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	452

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1dlfh_
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	d1dlfl_
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	1dlfH00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1dlfL00
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 (8)

;The pH-dependent structural variation of complementarity-determining region H3 in the crystal structures of the Fv fragment from an anti-dansyl monoclonal antibody. ;

J.Mol.Biol. (1999)

PMID: 10438610 · DOI: 10.1006/jmbi.1999.2931 PRIMARY

;Role of the Domain-Domain Interaction in the Construction of the Antigen Combining Site. A Comparative Study by 1H-15N Shift Correlation NMR Spectroscopy of the Fv and Fab Fragments of Anti-Dansyl Mouse Monoclonal Antibody ;

J.Mol.Biol. (1994)

Dynamical Structure of the Antibody Combining Site as Studied by 1H-15N Shift Correlation NMR Spectroscopy

Biochemistry (1992)

;Isotope-Edited Nuclear Magnetic Resonance Study of Fv Fragment of Anti-Dansyl Mouse Monoclonal Antibody: Recognition of the Dansyl Hapten ;

Biochemistry (1992)

;Preparation of the Fv Fragment from a Short-Chain Mouse Igg2A Anti-Dansyl Monoclonal Antibody and Use of Selectively Deuterated Fv Analogues for Two-Dimensional 1H NMR Analyses of the Antigen-Antibody Interactions ;

Biochemistry (1991)

Multinuclear NMR Study of the Structure of the Fv Fragment of Anti-Dansyl Mouse Igg2A Antibody

Biochemistry (1991)

Conformation and Stereoselective Reduction of Hapten Side Chain in the Antibody Combining Site

J.Am.Chem.Soc. (1991)

Structure of a Mouse Immunoglobulin G that Lacks the Entire Ch1 Domain: Protein Sequencing and Small-Angle X-Ray Scattering Studies

Biochemistry (1990)

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Unit-cell length a length_a	56.101 Å
Unit-cell length b length_b	70.722 Å
Unit-cell length c length_c	53.464 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1830
R_work r_work	0.1830
R_free r_free	0.2300

fit	/app/data/saxs_computation/dl/1dlf/1dlf.fit
pddf	/app/data/pr_computation/dl/1dlf/1dlf.pr.out
profile	/app/data/saxs_computation/dl/1dlf/1dlf.dat

HIGH RESOLUTION CRYSTAL STRUCTURE OF THE FV FRAGMENT FROM AN ANTI-DANSYL SWITCH VARIANT ANTIBODY IGG2A(S) CRYSTALLIZED AT PH 5.25

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

ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S)

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (8)

9. Files and Curves (10)

Files (7)

Curves (3)