SAXSdb — 5ji1

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

Growth/differentiation factor 8

Mus musculus

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 268–376 Chain B； UniProt 268–376	Fragment：UNP residues 268-376	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；100mM 2-(N-morpholino)ethanesulfonic acid pH 6.0, 40% 2-Methyl-2,4-pentanediol	Resolution 2.25 Å R-free 0.277

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 5JI1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3HH2 Crystal structure of the myostatin:follistatin 288 complex Deposited 2009-05-14	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 268–376（109 aa） Fragment：UNP residues 268-376 Chain B 268–376（109 aa） Fragment：UNP residues 268-376	Not recorded	PO4 PHOSPHATE ION × 3 CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；PEG 1000, Ethanol, Phosphate/citrate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.15 Å R-free 0.249
3SEK Crystal Structure of the Myostatin:Follistatin-like 3 Complex Deposited 2011-06-10	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 B 268–376（109 aa） Fragment：UNP Residues 268-376	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 7.5；293 K；potassium thiocyanate, PEG 3350, pH 7.5, hanging drop, temperature 293K	Resolution 2.40 Å R-free 0.270

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GDF8_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–109； UniProt 268–376 Author chain B； PDBConstruct 1–109； UniProt 268–376

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	5ji1
Deposition date deposition_date	2016-04-21
Structure title title	Crystal Structure of GDF8
Keywords keywords	GDF8, myostatin, TGFbeta, Ligand, CYTOKINE; CYTOKINE
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	21.06 Å
Radius of gyration Rg (electron density) rg_electron	20.58 Å
Forward intensity I(0) i0	8559270.00
Molecular weight molecular_weight	21458.0 kDa
Excluded volume excluded_volume	26690 Å³
Envelope volume envelope_volume	35486 Å³
Hydration-shell volume shell_volume	14863 Å³
Envelope diameter envelope_diameter	68.1 Å
Shell Rg shell_rg	26.30 Å
Envelope Rg envelope_rg	20.33 Å
Shape Rg shape_rg	20.67 Å
Total Rg total_rg	21.19 Å
Total atoms total_atoms	1491
Residues n_residues	187
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	65.8 Å
Rg (real space) rg_real	21.02 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	8.5590e+06
I(0) uncertainty (real space) i0_real_error	1.0670e+05
Rg (reciprocal space) rg_reciprocal	21.03 Å
I(0) (reciprocal space) i0_reciprocal	8559000.0000
Solution quality estimate total_estimate	0.8244
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	31.9 Å
Skewness Skewness skewness	0.101
Kurtosis Kurtosis kurtosis	-0.721
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1098000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.943; Smooth: 0.000

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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 8
Molecular weight formula_weight	12422.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1529

DFGLDCDEHSTESRCCRYPLTVDFEAFGWDWIIAPKRYKANYCSGECEFVFLQKYPHTHLVHQANPRGSAGPCCTPTKMSPINMLYFNGKEQIIYGKIPAMVVDRCGCS

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Cricetulus griseus

Entity 2 Entity 2 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	30

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5ji1a_
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

Domain ID domain_id	d5ji1b_
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

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8. Citations (1)

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Unit-cell length a length_a	29.606 Å
Unit-cell length b length_b	77.739 Å
Unit-cell length c length_c	119.544 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	36.965 Å
R factor r_factor	0.2377
R_work r_work	0.2348
R_free r_free	0.2773

fit	/app/data/saxs_computation/ji/5ji1/5ji1.fit
pddf	/app/data/pr_computation/ji/5ji1/5ji1.pr.out
profile	/app/data/saxs_computation/ji/5ji1/5ji1.dat

Crystal Structure of GDF8

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

Growth/differentiation factor 8

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