SAXSdb — 5vqf

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

Transforming growth factor beta-1

Sus scrofa

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Homooligomer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 30–390 Chain B； UniProt 30–390	Mutation：C4S, N147Q	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；7% PEG 3350, 17% isopropanol, 0.1m Na citrate pH 5.6	Resolution 2.90 Å R-free 0.280
2	Other combination Homooligomer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 30–390 Chain D； UniProt 30–390	Mutation：C4S, N147Q	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；7% PEG 3350, 17% isopropanol, 0.1m Na citrate pH 5.6	Resolution 2.90 Å R-free 0.280

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 5VQF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6UJA Integrin alpha-v beta-8 in complex with pro-TGF-beta1 Deposited 2019-10-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 30–390（361 aa）	Not recorded	CA CALCIUM ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TGFB1_PIG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–363； UniProt 30–390 Author chain B； PDBConstruct 3–363； UniProt 30–390 Author chain C； PDBConstruct 3–363； UniProt 30–390 Author chain D； PDBConstruct 3–363； UniProt 30–390

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	5vqf
Deposition date deposition_date	2017-05-08
Structure title title	Crystal Structure of pro-TGF-beta 1
Keywords keywords	pro-complex, latency, homodimer, PROTEIN BINDING; PROTEIN BINDING
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	46.22 Å
Radius of gyration Rg (electron density) rg_electron	46.93 Å
Forward intensity I(0) i0	345162000.00
Molecular weight molecular_weight	153050.0 kDa
Excluded volume excluded_volume	191970 Å³
Envelope volume envelope_volume	287890 Å³
Hydration-shell volume shell_volume	54211 Å³
Envelope diameter envelope_diameter	159.0 Å
Shell Rg shell_rg	46.87 Å
Envelope Rg envelope_rg	46.18 Å
Shape Rg shape_rg	46.87 Å
Total Rg total_rg	47.12 Å
Total atoms total_atoms	10753
Residues n_residues	1330
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	158.5 Å
Rg (real space) rg_real	46.66 Å
Rg uncertainty (real space) rg_real_error	1.92 Å
I(0) (real space) i0_real	3.4520e+08
I(0) uncertainty (real space) i0_real_error	6.9680e+06
Rg (reciprocal space) rg_reciprocal	46.22 Å
I(0) (reciprocal space) i0_reciprocal	345000000.0000
Solution quality estimate total_estimate	0.8196
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	42.0 Å
Skewness Skewness skewness	0.471
Kurtosis Kurtosis kurtosis	-0.607
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	27290000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.655; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.870; Smooth: 0.818

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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	Transforming growth factor beta-1
Molecular weight formula_weight	41432.4 kDa
Mutation mutation	C4S, N147Q
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
Atom count atom_count	10753

GPLSTSKTIDMELVKRKRIEAIRGQILSKLRLASPPSQGDVPPGPLPEAVLALYNSTRDRVAGESVEPEPEPEADYYAKEVTRVLMVESGNQIYDKFKGTPHSLYMLFNTSELREAVPEPVLLSRAELRLLRLKLKVEQHVELYQKYSQDSWRYLSNRLLAPSDSPEWLSFDVTGVVRQWLTRREAIEGFRLSAHCSCDSKDNTLHVEINGFNSGRRGDLATIHGMNRPFLLLMATPLERAQHLHSSRHRRALDTNYCFSSTEKNCCVRQLYIDFRKDLGWKWIHEPKGYHANFCLGPCPYIWSLDTQYSKVLALYNQHNPGASAAPCCVPQALEPLPIVYYVGRKPKVEQLSNMIVRSCKCS

来源 Source

来源生物 organism	Sus scrofa
通用名 common_name	Pig
NCBI Class编号 ncbi_taxonomy_id	9823
宿主生物 host_organism	Cricetulus griseus

Entity 2 Entity 2 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	2

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	5vqfA01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2330 —

Domain ID domain_id	5vqfA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	970 —

Domain ID domain_id	5vqfB01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2330 —

Domain ID domain_id	5vqfB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	970 —

Domain ID domain_id	5vqfC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	970 —

Domain ID domain_id	5vqfD01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	970 —

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8. Citations (2)

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Unit-cell length a length_a	54.660 Å
Unit-cell length b length_b	126.920 Å
Unit-cell length c length_c	137.920 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.70 °
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	2.900 Å
Low-resolution limit resolution_low	37.142 Å
R factor r_factor	0.2406
R_work r_work	0.2392
R_free r_free	0.2798

fit	/app/data/saxs_computation/vq/5vqf/5vqf.fit
pddf	/app/data/pr_computation/vq/5vqf/5vqf.pr.out
profile	/app/data/saxs_computation/vq/5vqf/5vqf.dat

Crystal Structure of pro-TGF-beta 1

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

Transforming growth factor beta-1

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