SAXSdb — 5e4g

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

Growth/differentiation factor 11

Homo sapiens

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 299–407	Fragment：UNP residues 299-407	PG4 TETRAETHYLENE GLYCOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.18 M magnesium acetate, 0.1 M HEPES, pH 7.5, 22.5% PEG3350, 0.01 M strontium chloride	Resolution 1.50 Å R-free 0.207

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 5E4G	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5JHW Crystal Structure of the GDF11:Follistatin 288 complex Deposited 2016-04-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 299–407（109 aa） Fragment：UNP residues 299-407 Chain B 299–407（109 aa） Fragment：UNP residues 299-407	Not recorded	PO4 PHOSPHATE ION × 3 FLC CITRATE ANION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；298 K；100mM Phosphate/Citrate pH 4.2, 14% EtOH, 1% PEG 1000	Resolution 2.35 Å R-free 0.247
5UHM Apo-Structure of Mature Growth Differentiation Factor 11 Deposited 2017-01-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 299–407（109 aa） Chain B 299–407（109 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.75；298.15 K；5mM Calcium Chloride 0.1M Sodium Acetate 33% MPD	Resolution 1.90 Å R-free 0.258
6MAC Ternary structure of GDF11 bound to ActRIIB-ECD and Alk5-ECD Deposited 2018-08-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 300–407（108 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；.05-.15M sodium acetate 12-24% polyethylene glycol 8000 .05-.15M sodium thiocyanate	Resolution 2.34 Å R-free 0.267
7MRZ Structure of GDF11 bound to fused ActRIIB-ECD and Alk4-ECD with Anti-ActRIIB Fab fragment Deposited 2021-05-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain A 299–407（109 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1M HEPES, 0.9M ammonium sulfate, 0.9 M KCl	Resolution 3.00 Å R-free 0.327

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GDF11_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–109； UniProt 299–407

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	5e4g
Deposition date deposition_date	2015-10-06
Structure title title	Crystal structure of human growth differentiation factor 11 (GDF-11)
Keywords keywords	Bone morphogenetic protein 11, BMP-11, GDF 11, HORMONE, growth factor; HORMONE
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	18.75 Å
Radius of gyration Rg (electron density) rg_electron	18.53 Å
Forward intensity I(0) i0	3348560.00
Molecular weight molecular_weight	12733.0 kDa
Excluded volume excluded_volume	15735 Å³
Envelope volume envelope_volume	20321 Å³
Hydration-shell volume shell_volume	10176 Å³
Envelope diameter envelope_diameter	67.0 Å
Shell Rg shell_rg	22.70 Å
Envelope Rg envelope_rg	19.00 Å
Shape Rg shape_rg	18.59 Å
Total Rg total_rg	19.11 Å
Total atoms total_atoms	885
Residues n_residues	108
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	67.0 Å
Rg (real space) rg_real	18.96 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	3.3490e+06
I(0) uncertainty (real space) i0_real_error	4.7200e+04
Rg (reciprocal space) rg_reciprocal	18.93 Å
I(0) (reciprocal space) i0_reciprocal	3349000.0000
Solution quality estimate total_estimate	0.8048
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.6 Å
Skewness Skewness skewness	0.486
Kurtosis Kurtosis kurtosis	-0.462
Angular range angular_range	— – 0.4250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	395600.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.709; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.406; Smooth: 0.925

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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	Growth/differentiation factor 11
Molecular weight formula_weight	12471.3 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	1069

NLGLDCDEHSSESRCCRYPLTVDFEAFGWDWIIAPKRYKANYCSGQCEYMFMQKYPHTHLVQQANPRGSAGPCCTPTKMSPINMLYFNDKQQIIYGKIPGMVVDRCGCS

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 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	142

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5e4ga_
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.17.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	5e4gA00
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 (1)

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Unit-cell length a length_a	32.270 Å
Unit-cell length b length_b	32.270 Å
Unit-cell length c length_c	210.602 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 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	22.818 Å
R factor r_factor	0.1890
R_work r_work	0.1880
R_free r_free	0.2071

fit	/app/data/saxs_computation/e4/5e4g/5e4g.fit
pddf	/app/data/pr_computation/e4/5e4g/5e4g.pr.out
profile	/app/data/saxs_computation/e4/5e4g/5e4g.dat

Crystal structure of human growth differentiation factor 11 (GDF-11)

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

Growth/differentiation factor 11

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