SAXSdb — 1bdv

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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 Homooligomer 蛋白 4 / DNA 2 / RNA 0 / 其他Polymer 0 PDB declaration: hexameric	Entity 1：;DNA (5'-D(TPAPTPAPGPTPAPGPAPGPTPGPCPTPTPCPTPAPTPCPAPT)-3') ; × 1 Entity 2：;DNA (5'-D(APAPTPGPAPTPAPGPAPAPGPCPAPCPTPCPTPAPCPTPAPT)-3') ; × 1 Entity 3：PROTEIN (ARC FV10 REPRESSOR) × 4 缺少 UniProt 身份时不显示参考序列区间	Entity 3Mutation：F10V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 2.80 Å R-free 0.301

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	1bdv
Deposition date deposition_date	1998-05-11
Structure title title	ARC FV10 COCRYSTAL
Keywords keywords	GENE-REGULATING PROTEIN, GENE REGULATION-DNA COMPLEX; GENE REGULATION/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	22.58 Å
Radius of gyration Rg (electron density) rg_electron	21.61 Å
Forward intensity I(0) i0	33401800.00
Molecular weight molecular_weight	35233.0 kDa
Excluded volume excluded_volume	40114 Å³
Envelope volume envelope_volume	50926 Å³
Hydration-shell volume shell_volume	20253 Å³
Envelope diameter envelope_diameter	75.8 Å
Shell Rg shell_rg	27.60 Å
Envelope Rg envelope_rg	21.72 Å
Shape Rg shape_rg	21.56 Å
Total Rg total_rg	22.34 Å
Total atoms total_atoms	2418
Residues n_residues	236
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	74.8 Å
Rg (real space) rg_real	22.64 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	3.3400e+07
I(0) uncertainty (real space) i0_real_error	4.7620e+05
Rg (reciprocal space) rg_reciprocal	22.63 Å
I(0) (reciprocal space) i0_reciprocal	33400000.0000
Solution quality estimate total_estimate	0.8849
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.8 Å
Skewness Skewness skewness	0.425
Kurtosis Kurtosis kurtosis	-0.331
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3753000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.858; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.964

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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	;DNA (5'-D(TPAPTPAPGPTPAPGPAPGPTPGPCPTPTPCPTPAPTPCPAPT)-3') ;
Molecular weight formula_weight	6756.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E
Atom count atom_count	2452

TATAGTAGAGTGCTTCTATCAT

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(APAPTPGPAPTPAPGPAPAPGPCPAPCPTPCPTPAPCPTPAPT)-3') ;
Molecular weight formula_weight	6743.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

AATGATAGAAGCACTCTACTAT

Entity 3 Entity 3 polymer

Description description	PROTEIN (ARC FV10 REPRESSOR)
Molecular weight formula_weight	6190.2 kDa
Mutation mutation	F10V
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D

MKGMSKMPQVNLRWPREVLDLVRKVAEENGRSVNSEIYQRVMESFKKEGRIGA

来源 Source

来源生物 organism	Enterobacteria phage P22
NCBI Class编号 ncbi_taxonomy_id	10754
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	34

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1bdva_
Class class	a — All alpha proteins
Fold Fold fold	a.43 — Ribbon-helix-helix
Superfamily Superfamily superfamily	a.43.1 — Ribbon-helix-helix
Family Family family	a.43.1.1 — Arc/Mnt-like phage repressors

Domain ID domain_id	d1bdvb_
Class class	a — All alpha proteins
Fold Fold fold	a.43 — Ribbon-helix-helix
Superfamily Superfamily superfamily	a.43.1 — Ribbon-helix-helix
Family Family family	a.43.1.1 — Arc/Mnt-like phage repressors

Domain ID domain_id	d1bdvc_
Class class	a — All alpha proteins
Fold Fold fold	a.43 — Ribbon-helix-helix
Superfamily Superfamily superfamily	a.43.1 — Ribbon-helix-helix
Family Family family	a.43.1.1 — Arc/Mnt-like phage repressors

Domain ID domain_id	d1bdvd_
Class class	a — All alpha proteins
Fold Fold fold	a.43 — Ribbon-helix-helix
Superfamily Superfamily superfamily	a.43.1 — Ribbon-helix-helix
Family Family family	a.43.1.1 — Arc/Mnt-like phage repressors

CATH v4.4 (4 domains)

Domain ID domain_id	1bdvA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1220 — Arc Repressor Mutant
Homologous superfamily homologous superfamily	10 — Met repressor-like

Domain ID domain_id	1bdvB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1220 — Arc Repressor Mutant
Homologous superfamily homologous superfamily	10 — Met repressor-like

Domain ID domain_id	1bdvC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1220 — Arc Repressor Mutant
Homologous superfamily homologous superfamily	10 — Met repressor-like

Domain ID domain_id	1bdvD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1220 — Arc Repressor Mutant
Homologous superfamily homologous superfamily	10 — Met repressor-like

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8. Citations (2)

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Unit-cell length a length_a	62.840 Å
Unit-cell length b length_b	56.310 Å
Unit-cell length c length_c	52.980 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.03 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2435
R_work r_work	0.2435
R_free r_free	0.3010

fit	/app/data/saxs_computation/bd/1bdv/1bdv.fit
pddf	/app/data/pr_computation/bd/1bdv/1bdv.pr.out
profile	/app/data/saxs_computation/bd/1bdv/1bdv.dat

ARC FV10 COCRYSTAL

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

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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)