SAXSdb — 9vjj

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1. Structure Basics

entry_id	9vjj
deposition_date	2025-06-20
title	Crystal Structure of human Latent TGF-beta1 in complex with SOF10
keywords	Latent TGF-beta1, Cytokine, Fab, antibody, fibrosis; CYTOKINE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	32.70 Å
rg_electron	31.98 Å
i0	227356000.00
molecular_weight	119510.0 kDa
excluded_volume	148990 Å³
envelope_volume	189340 Å³
shell_volume	48956 Å³
envelope_diameter	114.3 Å
shell_rg	39.29 Å
envelope_rg	31.44 Å
shape_rg	31.97 Å
total_rg	32.59 Å
total_atoms	8414
n_residues	1077
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	107.1 Å
rg_real	32.50 Å
rg_real_error	0.66 Å
i0_real	2.2740e+08
i0_real_error	3.1390e+06
rg_reciprocal	32.58 Å
i0_reciprocal	227400000.0000
total_estimate	0.8824
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	42.4 Å
skewness	0.186
kurtosis	-0.310
angular_range	— – 0.2400 Å⁻¹
current_alpha	0.0000
highest_alpha	42650000.0000
n_real_points	49
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.829; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.983

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Transforming growth factor beta-1 proprotein
formula_weight	42304.1 kDa
mutation	C33S
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	8418

DYKDDDDKLSTSKTIDMELVKRKRIEAIRGQILSKLRLASPPSQGEVPPGPLPEAVLALYNSTRDRVAGESAEPEPEPEADYYAKEVTRVLMVETHNEIYDKFKQSTHSIYMFFNTSELREAVPEPVLLSRAELRLLRLKLKVEQHVELYQKYSNNSWRYLSNRLLAPSDSPEWLSFDVTGVVRQWLSRGGEIEGFRLSAHCSCDSRDNTLQVDINGFTTGRRGDLATIHGMNRPFLLLMATPLERAQHLQSSRHRRALDTNYCFSSTEKNCCVRQLYIDFRKDLGWKWIHEPKGYHANFCLGPCPYIWSLDTQYSKVLALYNQHNPGASAAPCCVPQALEPLPIVYYVGRKPKVEQLSNMIVRSCKCS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	SOF10 Fab heavy chain
formula_weight	24512.5 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	H,I

QVQLVESGGGVVQPGRSLRLSCAASGFTFSSEAMNWIRQPPGKGLEWIGYIYTSGTTYRANWARGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARGTGIYDYYYWVMDLWGPGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

Entity 3 polymer

description	SOF10 Fab light chain
formula_weight	23271.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	L,M

DIQMTQSPSSLSASVGDRVTITCQASQSISTYLAWYQQKPGQPPKLLIYAASTLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQSYSDGDSVGFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

Entity 4 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	4

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	4

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6. Citations (1)

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length_a	225.878 Å
length_b	91.707 Å
length_c	126.120 Å
angle_alpha	90.00 °
angle_beta	108.58 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.477 Å
resolution_low	36.120 Å
r_factor	0.2827
r_work	0.2813
r_free	0.3098

fit	/app/data/saxs_computation/vj/9vjj/9vjj.fit
pddf	/app/data/pr_computation/vj/9vjj/9vjj.pr.out
profile	/app/data/saxs_computation/vj/9vjj/9vjj.dat

Crystal Structure of human Latent TGF-beta1 in complex with SOF10

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 branched

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)