SAXSdb — 4ycg

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

Bone Morphogenetic Protein 9 Growth Factor Domain

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	Other combination Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 23–318 Chain B； UniProt 23–318	Not recorded	Bone Morphogenetic Protein 9 Prodomain × 2 （Q9UK05） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZN ZINC ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；0.15 M zinc acetate, 0.1 M sodium cacodylate pH 5.8, 4% isopropanol, 0.15 M nondetergent sulfobetaine (NDSB-211)	Resolution 3.30 Å R-free 0.230

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 4YCG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4YCI non-latent pro-bone morphogenetic protein 9 Deposited 2015-02-20	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 23–318（296 aa） Chain B 23–318（296 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ZN ZINC ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；0.15 M zinc acetate, 0.1 M sodium cacodylate pH 5.8, 4% isopropanol, 0.15 M nondetergent sulfobetaine (NDSB-211)	Resolution 3.25 Å R-free 0.260

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

View Construct and Data Evidence

UniProt name	GDF2_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–296； UniProt 23–318 Author chain B； PDBConstruct 1–296； UniProt 23–318

Bone Morphogenetic Protein 9 Prodomain

Homo sapiens

UniProt Q9UK05

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 Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 320–429 Chain D； UniProt 320–429	Not recorded	Bone Morphogenetic Protein 9 Growth Factor Domain × 2 （Q9WV56） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZN ZINC ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；0.15 M zinc acetate, 0.1 M sodium cacodylate pH 5.8, 4% isopropanol, 0.15 M nondetergent sulfobetaine (NDSB-211)	Resolution 3.30 Å R-free 0.230

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 4YCG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ZKZ Crystal Structure of BMP9 Deposited 2005-05-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 320–429（110 aa） Fragment：Growth/differentiation factor 2, residues 320-429	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；1-1.2 M Sodium Chloride, 7-10 mM Hexadecyltrimethylammonium Bromide 10 mM Magnesium Chloride, pH 7.5, temperature 296K, VAPOR DIFFUSION, HANGING DROP	Resolution 2.33 Å R-free 0.272
4FAO Specificity and Structure of a high affinity Activin-like 1 (ALK1) signaling complex Deposited 2012-05-22	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 320–429（110 aa） Chain B 320–429（110 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；20% PEG 3350, 0.2 M sodium malonate, 0.1 M Bis-Tris propane, pH 6.5, vapor diffusion, temperature 293K	Resolution 3.36 Å R-free 0.261
4FAO Specificity and Structure of a high affinity Activin-like 1 (ALK1) signaling complex Deposited 2012-05-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 320–429（110 aa） Chain H 320–429（110 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；20% PEG 3350, 0.2 M sodium malonate, 0.1 M Bis-Tris propane, pH 6.5, vapor diffusion, temperature 293K	Resolution 3.36 Å R-free 0.261
4FAO Specificity and Structure of a high affinity Activin-like 1 (ALK1) signaling complex Deposited 2012-05-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain M 320–429（110 aa） Chain N 320–429（110 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；20% PEG 3350, 0.2 M sodium malonate, 0.1 M Bis-Tris propane, pH 6.5, vapor diffusion, temperature 293K	Resolution 3.36 Å R-free 0.261
4FAO Specificity and Structure of a high affinity Activin-like 1 (ALK1) signaling complex Deposited 2012-05-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain S 320–429（110 aa） Chain T 320–429（110 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；20% PEG 3350, 0.2 M sodium malonate, 0.1 M Bis-Tris propane, pH 6.5, vapor diffusion, temperature 293K	Resolution 3.36 Å R-free 0.261
4FAO Specificity and Structure of a high affinity Activin-like 1 (ALK1) signaling complex Deposited 2012-05-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain a 320–429（110 aa） Chain b 320–429（110 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；20% PEG 3350, 0.2 M sodium malonate, 0.1 M Bis-Tris propane, pH 6.5, vapor diffusion, temperature 293K	Resolution 3.36 Å R-free 0.261
4FAO Specificity and Structure of a high affinity Activin-like 1 (ALK1) signaling complex Deposited 2012-05-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain g 320–429（110 aa） Chain h 320–429（110 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；20% PEG 3350, 0.2 M sodium malonate, 0.1 M Bis-Tris propane, pH 6.5, vapor diffusion, temperature 293K	Resolution 3.36 Å R-free 0.261
4MPL Crystal structure of BMP9 at 1.90 Angstrom Deposited 2013-09-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 321–429（109 aa） Fragment：UNP residues 321-429	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；0.12M magnesium nitrate, 12% PEG3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.224
4YCI non-latent pro-bone morphogenetic protein 9 Deposited 2015-02-20	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 320–429（110 aa） Chain D 320–429（110 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ZN ZINC ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；0.15 M zinc acetate, 0.1 M sodium cacodylate pH 5.8, 4% isopropanol, 0.15 M nondetergent sulfobetaine (NDSB-211)	Resolution 3.25 Å R-free 0.260
5HZW Crystal structure of the orphan region of human endoglin/CD105 in complex with BMP9 Deposited 2016-02-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 320–429（110 aa） Fragment：UNP residues 320-429	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.1 M AMMONIUM TARTRATE	Resolution 4.45 Å R-free 0.318
5I05 Crystal structure of human BMP9 at 1.87 A resolution Deposited 2016-02-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 320–429（110 aa） Fragment：UNP residues 320-429	Not recorded	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；293 K；1.0 M LiCl, 4% (v/v) PEG6000, 0.1 M NA-CITRATE	Resolution 1.87 Å R-free 0.233
6SF2 Ternary complex of human bone morphogenetic protein 9 (BMP9) growth factor domain, its prodomain and extracellular domain of activin receptor-like kinase 1 (ALK1). Deposited 2019-07-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 320–429（110 aa） Chain C 23–319（297 aa） Chain E 320–429（110 aa） Chain F 23–319（297 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.14 M potassium sodium tartrate, 14% PEG 3350	Resolution 3.30 Å R-free 0.274
9DPM BMP-9 Monomer Growth Factor with Cysteinylation Deposited 2024-09-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 320–429（110 aa）	Mutation：A321S	CYS CYSTEINE × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289.15 K；0.9 M sodium chloride, 133 mM HEPES, 166 mM MES	Resolution 1.90 Å R-free 0.242
9DPN BMP-9 Wild-Type Dimer Without Radiation Damage in Neutral pH Deposited 2024-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 320–429（110 aa）	Mutation：A321S	GOL GLYCEROL × 2 CL CHLORIDE ION × 10 NA SODIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289.15 K；1M NaCl, 17% Glycerol, 0.1 M HEPEs pH 7.5	Resolution 2.24 Å R-free 0.206
9DPO BMP-9 Wild-Type Dimer With Radiation Damage in Neutral pH Deposited 2024-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 320–429（110 aa）	Mutation：A321S	CL CHLORIDE ION × 10 NA SODIUM ION × 8 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289.15 K；1M NaCl, 17% Glycerol, 0.1 M HEPEs pH 7.5	Resolution 2.34 Å R-free 0.245
9DPP BMP-9 Wild-Type Dimer in Acidic pH Deposited 2024-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 320–429（110 aa）	Mutation：A321S	GOL GLYCEROL × 4 CL CHLORIDE ION × 18 NA SODIUM ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；289.15 K；1M NaCl, 3.5% PEG8K, 0.3M Citrate pH 3.5	Resolution 2.12 Å R-free 0.258
9DPQ BMP-9 Wild-Type Dimer without Radiation Damage in Acidic pH Deposited 2024-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 320–429（110 aa）	Mutation：A321S	GOL GLYCEROL × 4 CL CHLORIDE ION × 20 NA SODIUM ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；289.15 K；1M NaCl, 3.5% PEG8K, 0.3M Sodium Citrate pH 3.5	Resolution 2.35 Å R-free 0.249
9DPR BMP-9 Wild-Type Dimer with Radiation Damage in Acidic pH Deposited 2024-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 320–429（110 aa）	Mutation：A321S	GOL GLYCEROL × 2 CL CHLORIDE ION × 20 NA SODIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；289.15 K；1M NaCl, 3.5% PEG8K, 0.3M Sodium Citrate pH 3.5	Resolution 2.61 Å R-free 0.266
9DPS BMP-9 G389S Dimer Without Radiation Damage in Neutral pH Deposited 2024-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 320–429（110 aa）	Mutation：A321S, G389S	CL CHLORIDE ION × 12 NA SODIUM ION × 8 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289.15 K；1M NaCl, 22-26% glycerol, 0.1 M HEPES pH 7.5	Resolution 2.06 Å R-free 0.249
9DPT BMP-9 G389S Dimer With Radiation Damage in Neutral pH Deposited 2024-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 320–429（110 aa）	Mutation：A321S, G389S	CL CHLORIDE ION × 10 NA SODIUM ION × 8 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289.15 K；1M NaCl, 22-26% glycerol, 0.1 M HEPEs pH 7.5	Resolution 2.49 Å R-free 0.279
9DPU BMP-9 G389S Dimer in Acidic pH Deposited 2024-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 320–429（110 aa）	Mutation：A321S, G389S	CL CHLORIDE ION × 10 NA SODIUM ION × 2 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；1M NaCl, 0.1M Acetic Acid pH 4, 27% Glycerol	Resolution 2.10 Å R-free 0.224
9DPV BMP-9 K357R G389S Dimer Without Radiation Damage in Neutral pH Deposited 2024-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 320–429（110 aa）	Mutation：A321S, K357R, G389S	GOL GLYCEROL × 2 CL CHLORIDE ION × 10 NA SODIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289.15 K；1M NaCl, 22-26% glycerol, 0.1 M HEPES pH 7.5	Resolution 1.99 Å R-free 0.265
9DPW BMP-9 K357R G389S Dimer With Radiation Damage in Neutral pH Deposited 2024-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 320–429（110 aa）	Mutation：A321S, K357R, G389S	GOL GLYCEROL × 4 CL CHLORIDE ION × 18 NA SODIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289.15 K；1M NaCl, 22-26% glycerol, 0.1 M HEPES pH 7.5	Resolution 2.71 Å R-free 0.299
9DPX BMP-9 G389S K357R Dimer in Acidic pH Deposited 2024-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 320–429（110 aa）	Mutation：A321S, K357R, G389S	GOL GLYCEROL × 4 CL CHLORIDE ION × 12 NA SODIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；1M NaCl , 0.1M Acetic Acid pH 4, 32% Glycerol	Resolution 2.10 Å R-free 0.268

19 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GDF2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–110； UniProt 320–429 Author chain D； PDBConstruct 1–110； UniProt 320–429

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	4ycg
Deposition date deposition_date	2015-02-20
Structure title title	Pro-bone morphogenetic protein 9
Keywords keywords	pro-BMP complex, morphogen, transforming growth factor-beta family, 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	38.04 Å
Radius of gyration Rg (electron density) rg_electron	37.86 Å
Forward intensity I(0) i0	79986000.00
Molecular weight molecular_weight	69806.0 kDa
Excluded volume excluded_volume	86275 Å³
Envelope volume envelope_volume	118620 Å³
Hydration-shell volume shell_volume	28033 Å³
Envelope diameter envelope_diameter	139.0 Å
Shell Rg shell_rg	40.40 Å
Envelope Rg envelope_rg	37.55 Å
Shape Rg shape_rg	37.82 Å
Total Rg total_rg	38.13 Å
Total atoms total_atoms	4868
Residues n_residues	606
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	130.4 Å
Rg (real space) rg_real	38.59 Å
Rg uncertainty (real space) rg_real_error	1.50 Å
I(0) (real space) i0_real	7.9990e+07
I(0) uncertainty (real space) i0_real_error	1.3660e+06
Rg (reciprocal space) rg_reciprocal	38.25 Å
I(0) (reciprocal space) i0_reciprocal	79960000.0000
Solution quality estimate total_estimate	0.7662
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.8 Å
Skewness Skewness skewness	0.493
Kurtosis Kurtosis kurtosis	-0.512
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6942000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.641; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.510; Smooth: 0.523

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Bone Morphogenetic Protein 9 Growth Factor Domain
Molecular weight formula_weight	33224.8 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	4889

KPLQNWEQASPGENAHSSLGLSGAGEEGVFDLQMFLENMKVDFLRSLNLSGIPSQDKTRAEPPQYMIDLYNRYTTDKSSTPASNIVRSFSVEDAISTAATEDFPFQKHILIFNISIPRHEQITRAELRLYVSCQNDVDSTHGLEGSMVVYDVLEDSETWDQATGTKTFLVSQDIRDEGWETLEVSSAVKRWVRADSTTNKNKLEVTVQSHRESCDTLDISVPPGSKNLPFFVVFSNDRSNGTKETRLELKEMIGHEQETMLVKTAKNAYQVAGESQEEEGLDGYTAVGPLLARRKR

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 polymer

Description description	Bone Morphogenetic Protein 9 Prodomain
Molecular weight formula_weight	12103.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

SAGAGSHCQKTSLRVNFEDIGWDSWIIAPKEYEAYECKGGCFFPLADDVTPTKHAIVQTLVHLKFPTKVGKACCVPTKLSPISVLYKDDMGVPTLKYHYEGMSVAECGCR

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	Cricetulus griseus

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

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	21

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4ycgC00
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	4ycgD00
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	120.780 Å
Unit-cell length b length_b	120.780 Å
Unit-cell length c length_c	220.620 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	48.788 Å
R factor r_factor	0.2138
R_work r_work	0.2129
R_free r_free	0.2295

fit	/app/data/saxs_computation/yc/4ycg/4ycg.fit
pddf	/app/data/pr_computation/yc/4ycg/4ycg.pr.out
profile	/app/data/saxs_computation/yc/4ycg/4ycg.dat

Pro-bone morphogenetic protein 9

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

Bone Morphogenetic Protein 9 Growth Factor Domain

State in the Current Structure

Other States of the Same Protein in the Database

Bone Morphogenetic Protein 9 Prodomain

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

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)