SAXSdb — 1b8m

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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 (BRAIN DERIVED NEUROTROPHIC FACTOR) × 1 Entity 2：PROTEIN (NEUROTROPHIN-4) × 1 缺少 UniProt 身份时不显示参考序列区间	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；pH 6.0	Resolution 2.75 Å R-free 0.279

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	1b8m
Deposition date deposition_date	1999-02-01
Structure title title	BRAIN DERIVED NEUROTROPHIC FACTOR, NEUROTROPHIN-4
Keywords keywords	COMPLEX (GROWTH FACTOR-GROWTH FACTOR), NEUROTROPHIN, GROWTH FACTOR-NEUROTROPHIN-4 COMPLEX; GROWTH FACTOR/NEUROTROPHIN-4
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	20.73 Å
Radius of gyration Rg (electron density) rg_electron	19.93 Å
Forward intensity I(0) i0	11999400.00
Molecular weight molecular_weight	24624.0 kDa
Excluded volume excluded_volume	30394 Å³
Envelope volume envelope_volume	38911 Å³
Hydration-shell volume shell_volume	17102 Å³
Envelope diameter envelope_diameter	70.0 Å
Shell Rg shell_rg	25.42 Å
Envelope Rg envelope_rg	20.27 Å
Shape Rg shape_rg	19.92 Å
Total Rg total_rg	20.77 Å
Total atoms total_atoms	1721
Residues n_residues	224
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	70.5 Å
Rg (real space) rg_real	20.77 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	1.2000e+07
I(0) uncertainty (real space) i0_real_error	1.3490e+05
Rg (reciprocal space) rg_reciprocal	20.77 Å
I(0) (reciprocal space) i0_reciprocal	12000000.0000
Solution quality estimate total_estimate	0.8789
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	22.5 Å
Skewness Skewness skewness	0.407
Kurtosis Kurtosis kurtosis	-0.292
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	1702000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.830; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.947; Smooth: 0.986

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	PROTEIN (BRAIN DERIVED NEUROTROPHIC FACTOR)
Molecular weight formula_weight	13535.6 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	1778

HSDPARRGELSVCDSISEWVTAADKKTAVDMSGGTVTVLEKVPVSKGQLKQYFYETKCNPMGYTKEGCRGIDKRHWNSQCRTTQSYVRALTMDSKKRIGWRFIRIDTSCVCTLTIKRGR

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	PROTEIN (NEUROTROPHIN-4)
Molecular weight formula_weight	13944.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GVSETAPASRRGELAVCDAVSGWVTDRRTAVDLRGREVEVLGEVPAAGGSPLRQYFFETRCKADNAEEGGPGAGGGGCRGVDRRHWVSECKAKQSYVRALTADAQGRVGWRWIRIDTACVCTLLSRTGRA

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	57

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1b8ma_
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.3 — Neurotrophin

Domain ID domain_id	d1b8mb_
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.3 — Neurotrophin

CATH v4.4 (2 domains)

Domain ID domain_id	1b8mA00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

Domain ID domain_id	1b8mB00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

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8. Citations (3)

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Unit-cell length a length_a	50.700 Å
Unit-cell length b length_b	105.900 Å
Unit-cell length c length_c	51.800 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1980
R_free r_free	0.2790

fit	/app/data/saxs_computation/b8/1b8m/1b8m.fit
pddf	/app/data/pr_computation/b8/1b8m/1b8m.pr.out
profile	/app/data/saxs_computation/b8/1b8m/1b8m.dat

BRAIN DERIVED NEUROTROPHIC FACTOR, NEUROTROPHIN-4

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)