SAXSdb — 1bvo

▼

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

TRANSCRIPTION FACTOR GAMBIF1

Anopheles gambiae

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–DNA Homooligomer Protein × 2 DNA 4 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain A； UniProt 48–222	Fragment：SPECIFICITY DOMAIN	DNA DUPLEX × 2 DNA DUPLEX × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.6；pH 5.6	Resolution 2.70 Å R-free 0.288

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	Q17034_ANOGA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–175； UniProt 48–222

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	1bvo
Deposition date deposition_date	1998-09-16
Structure title title	DORSAL HOMOLOGUE GAMBIF1 BOUND TO DNA
Keywords keywords	;TRANSCRIPTION FACTOR, REL PROTEIN, MORPHOGEN, IMMUNITY, DEVELOPMENT, INSECTS, COMPLEX (TRANSCRIPTION FACTOR-DNA), COMPLEX (TRANSCRIPTION FACTOR-DNA) complex ;; COMPLEX (TRANSCRIPTION FACTOR/DNA)
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	21.28 Å
Radius of gyration Rg (electron density) rg_electron	20.30 Å
Forward intensity I(0) i0	20815200.00
Molecular weight molecular_weight	28756.0 kDa
Excluded volume excluded_volume	33335 Å³
Envelope volume envelope_volume	37166 Å³
Hydration-shell volume shell_volume	17037 Å³
Envelope diameter envelope_diameter	79.4 Å
Shell Rg shell_rg	24.83 Å
Envelope Rg envelope_rg	19.88 Å
Shape Rg shape_rg	20.26 Å
Total Rg total_rg	20.90 Å
Total atoms total_atoms	1986
Residues n_residues	205
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	76.6 Å
Rg (real space) rg_real	21.36 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	2.0820e+07
I(0) uncertainty (real space) i0_real_error	2.8010e+05
Rg (reciprocal space) rg_reciprocal	21.35 Å
I(0) (reciprocal space) i0_reciprocal	20820000.0000
Solution quality estimate total_estimate	0.8564
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.8 Å
Skewness Skewness skewness	0.419
Kurtosis Kurtosis kurtosis	-0.070
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	448000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.749; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.893; Smooth: 0.988

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	DNA DUPLEX
Molecular weight formula_weight	4585.0 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	2022

CTGGGAATTTCCCAG

Entity 2 Entity 2 polymer

Description description	DNA DUPLEX
Molecular weight formula_weight	4594.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

CTGGGTTAAACCCAG

Entity 3 Entity 3 polymer

Description description	TRANSCRIPTION FACTOR GAMBIF1
Molecular weight formula_weight	19627.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

PYVEITEQPHPKALRFRYECEGRSAGSIPGVNTTAEQKTFPSIQVHGYRGRAVVVVSCVTKEGPEHKPHPHNLVGKEGCKKGVCTVEINSTTMSYTFNNLGIQCVKKKDVEEALRLRQEIRVDPFRTGFGHAKEPGSIDLNAVRLCFQVFLEGQQRGRFTEPLTPVVSDIIYDKK

来源 Source

来源生物 organism	Anopheles gambiae
通用名 common_name	African malaria mosquito
NCBI Class编号 ncbi_taxonomy_id	7165
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	36

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1bvoa_
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.5 — p53-like transcription factors
Family Family family	b.2.5.3 — Rel/Dorsal transcription factors, DNA-binding domain

CATH v4.4 (1 domains)

Domain ID domain_id	1bvoA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	340 — Rel homology domain (RHD), DNA-binding domain

▶

8. Citations (1)

▶

Unit-cell length a length_a	87.610 Å
Unit-cell length b length_b	87.610 Å
Unit-cell length c length_c	96.160 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 43 2 2
Space-group number int_tables_number	95
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2190
R_work r_work	0.2190
R_free r_free	0.2880

fit	/app/data/saxs_computation/bv/1bvo/1bvo.fit
pddf	/app/data/pr_computation/bv/1bvo/1bvo.pr.out
profile	/app/data/saxs_computation/bv/1bvo/1bvo.dat

DORSAL HOMOLOGUE GAMBIF1 BOUND TO DNA

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

TRANSCRIPTION FACTOR GAMBIF1

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 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)