SAXSdb — 1bfv

▼

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

FV4155

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 L； UniProt 1–113	Fragment：MONOCLONAL ANTIBODY FV FRAGMENT	FV4155 × 1 ZN ZINC ION × 3 STG ESTRIOL 3-(B-D-GLUCURONIDE) × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 18% (W/V) PEG 8000, 200MM ZN ACETATE AND 100MM NA CACODYLATE, PH 7.5	Resolution 2.10 Å R-free 0.271
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain L； UniProt 1–113	Fragment：MONOCLONAL ANTIBODY FV FRAGMENT	FV4155 × 2 ZN ZINC ION × 6 STG ESTRIOL 3-(B-D-GLUCURONIDE) × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 18% (W/V) PEG 8000, 200MM ZN ACETATE AND 100MM NA CACODYLATE, PH 7.5	Resolution 2.10 Å R-free 0.271
3	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain L； UniProt 1–113	Fragment：MONOCLONAL ANTIBODY FV FRAGMENT	FV4155 × 2 ZN ZINC ION × 6 STG ESTRIOL 3-(B-D-GLUCURONIDE) × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 18% (W/V) PEG 8000, 200MM ZN ACETATE AND 100MM NA CACODYLATE, PH 7.5	Resolution 2.10 Å R-free 0.271
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain L； UniProt 1–113	Fragment：MONOCLONAL ANTIBODY FV FRAGMENT	FV4155 × 1 ZN ZINC ION × 3 STG ESTRIOL 3-(B-D-GLUCURONIDE) × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 18% (W/V) PEG 8000, 200MM ZN ACETATE AND 100MM NA CACODYLATE, PH 7.5	Resolution 2.10 Å R-free 0.271

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 1BFV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CFV MONOCLONAL ANTIBODY FRAGMENT FV4155 FROM E. COLI Deposited 1997-04-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 1–113（113 aa） Fragment：FV FRAGMENT	Not recorded	ZN ZINC ION × 3 E3G ESTRONE BETA-D-GLUCURONIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PROTEIN WAS CRYSTALLIZED FROM 18% (W/V) PEG 8000, 200MM ZN ACETATE AND 100MM NA CACODYLATE, PH 7.0	Resolution 2.10 Å R-free 0.247
1MAJ SOLUTION STRUCTURE OF AN ISOLATED ANTIBODY VL DOMAIN Deposited 1993-09-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–113（113 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1MAK SOLUTION STRUCTURE OF AN ISOLATED ANTIBODY VL DOMAIN Deposited 1993-09-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–113（113 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1SVZ Crystal structure of the single-chain Fv fragment 1696 in complex with the epitope peptide corresponding to N-terminus of HIV-2 protease Deposited 2004-03-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 4–112（109 aa） Fragment：scFv1696 Chain B 4–112（109 aa） Fragment：scFv1696	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；292 K；protein concentration 14mg/ml, 0.05M tri-sodium citrate, 0.1M sodium phosphate, 27% PEG 3400, 0.2M ammonium sulfate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.89 Å R-free 0.239
2BFV MONOCLONAL ANTIBODY FRAGMENT FV4155 FROM E. COLI Deposited 1997-05-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 1–113（113 aa） Fragment：MONOCLONAL ANTIBODY FV FRAGMENT	Not recorded	STG ESTRIOL 3-(B-D-GLUCURONIDE) × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；PROTEIN WAS CRYSTALLIZED FROM 15% (W/V) PEG 4000, 100MM NA ACETATE AND 50MM TRIS HCL PH 8.5	Resolution 2.50 Å
2DLF HIGH RESOLUTION CRYSTAL STRUCTURE OF THE FV FRAGMENT FROM AN ANTI-DANSYL SWITCH VARIANT ANTIBODY IGG2A(S) CRYSTALLIZED AT PH 6.75 Deposited 1998-12-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 1–113（113 aa） Fragment：FV FRAGMENT (VL DOMAIN) SYNONYM: ANTI-DANSYL FV FRAGMENT	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.75；CRYSTALLIZATION CONDITIONS: TEMPERATURE AT 20C. PRECIPITANT SOLUTION CONTAINED 1 AMMONIUM SULFATE AND 0.025 M SODIUM CACODYLATE (PH 6.75). 5 MG/ML OF FV FRAGMENT., VAPOR DIFFUSION, HANGING DROP	Resolution 1.55 Å R-free 0.233

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KV2G_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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1bfv
Deposition date deposition_date	1997-05-27
Structure title title	MONOCLONAL ANTIBODY FRAGMENT FV4155 FROM E. COLI
Keywords keywords	IMMUNOGLOBULIN, FV FRAGMENT, STEROID HORMONE, FINE SPECIFICITY; IMMUNOGLOBULIN
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	18.65 Å
Radius of gyration Rg (electron density) rg_electron	17.48 Å
Forward intensity I(0) i0	12405500.00
Molecular weight molecular_weight	26149.0 kDa
Excluded volume excluded_volume	32589 Å³
Envelope volume envelope_volume	36250 Å³
Hydration-shell volume shell_volume	17433 Å³
Envelope diameter envelope_diameter	59.5 Å
Shell Rg shell_rg	23.60 Å
Envelope Rg envelope_rg	17.78 Å
Shape Rg shape_rg	17.44 Å
Total Rg total_rg	18.49 Å
Total atoms total_atoms	1830
Residues n_residues	232
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	58.1 Å
Rg (real space) rg_real	18.55 Å
Rg uncertainty (real space) rg_real_error	0.21 Å
I(0) (real space) i0_real	1.2410e+07
I(0) uncertainty (real space) i0_real_error	1.2790e+05
Rg (reciprocal space) rg_reciprocal	18.56 Å
I(0) (reciprocal space) i0_reciprocal	12410000.0000
Solution quality estimate total_estimate	0.9021
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.9 Å
Skewness Skewness skewness	0.173
Kurtosis Kurtosis kurtosis	-0.435
Angular range angular_range	— – 0.4250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3540000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.964

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	FV4155
Molecular weight formula_weight	12438.0 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	2012

DIELTQSPPSLPVSLGDQVSISCRSSQSLVSNNRRNYLHWYLQKPGQSPKLVIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVAAEDLGLYFCSQSSHVPLTFGSGTKLEIKR

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
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	FV4155
Molecular weight formula_weight	13191.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QVQLQESGGGLVNLGGSMTLSCVASGFTFNTYYMSWVRQTPEKTLELVAAINSDGEPIYYPDTLKGRVTISRDNAKKTLYLQMSSLNFEDTALYYCARLNYAVYGMDYWGQGTTVTVSS

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
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	ESTRIOL 3-(B-D-GLUCURONIDE)
Molecular weight formula_weight	464.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	182

▼

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1bfvh1
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	d1bfvh2
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

Domain ID domain_id	d1bfvl_
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	1bfvH00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1bfvL00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

8. Citations (1)

▶

Unit-cell length a length_a	89.900 Å
Unit-cell length b length_b	89.900 Å
Unit-cell length c length_c	59.900 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	8

Space group space_group	P 4 21 2
Space-group number int_tables_number	90
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	—
R_work r_work	0.1870
R_free r_free	0.2710

fit	/app/data/saxs_computation/bf/1bfv/1bfv.fit
pddf	/app/data/pr_computation/bf/1bfv/1bfv.pr.out
profile	/app/data/saxs_computation/bf/1bfv/1bfv.dat

MONOCLONAL ANTIBODY FRAGMENT FV4155 FROM E. COLI

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

FV4155

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 (5)

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 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)