SAXSdb — 2r53

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

Bone morphogenetic protein 6

Homo sapiens

UniProt P22004

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 411–513 Chain B； UniProt 411–513	Fragment：BMP-6 variant B2, mature part	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；25% 2-Methyl-2,4-pentandiol, 0.1M sodium citrate pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.279

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 2R53	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2QCW Crystal Structure of Bone Morphogenetic Protein-6 (BMP-6) Deposited 2007-06-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 382–513（132 aa） Chain B 382–513（132 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；15% 2-methyl-2,4-pentanediol (MPD), 0.2 M Tri-Na Citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.49 Å R-free 0.276
2R52 Crystal structure analysis of Bone Morphogenetic Protein-6 (BMP-6) Deposited 2007-09-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 375–513（139 aa） Fragment：Mature part (residues 375-513) Chain B 375–513（139 aa） Fragment：Mature part (residues 375-513)	Not recorded	IPA ISOPROPYL ALCOHOL × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；20% 2-propanol, 0.1M sodium citrate pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.270
6OMO Human BMP6 homodimer Deposited 2019-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain I 410–513（104 aa） Chain J 410–513（104 aa）	Not recorded	IPA ISOPROPYL ALCOHOL × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100mM Tris HCl 8.0, 15% MPD	Resolution 2.80 Å R-free 0.244
9N4K CryoEM structure of ALK2-ActRIIB bound to BMP6 Deposited 2025-02-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 375–513（139 aa） Chain E 375–513（139 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 BMA beta-D-mannopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50mM Tris-HCL, 100mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å

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

View Construct and Data Evidence

UniProt name	BMP6_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 14–116； UniProt 411–513 Author chain B； PDBConstruct 14–116； UniProt 411–513

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	2r53
Deposition date deposition_date	2007-09-03
Structure title title	Crystal structure analysis of Bone Morphogenetic Protein-6 variant B2 (B2-BMP-6)
Keywords keywords	;BMP6, Vgr, TGF-beta ligand, Chondrogenesis, Cleavage on pair of basic residues, Cytokine, Developmental protein, Differentiation, Glycoprotein, Growth factor, Osteogenesis, Secreted ;; 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	21.16 Å
Radius of gyration Rg (electron density) rg_electron	21.26 Å
Forward intensity I(0) i0	11036700.00
Molecular weight molecular_weight	24768.0 kDa
Excluded volume excluded_volume	31081 Å³
Envelope volume envelope_volume	39207 Å³
Hydration-shell volume shell_volume	16793 Å³
Envelope diameter envelope_diameter	81.1 Å
Shell Rg shell_rg	26.02 Å
Envelope Rg envelope_rg	21.62 Å
Shape Rg shape_rg	21.36 Å
Total Rg total_rg	21.68 Å
Total atoms total_atoms	1732
Residues n_residues	214
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	79.9 Å
Rg (real space) rg_real	21.42 Å
Rg uncertainty (real space) rg_real_error	0.85 Å
I(0) (real space) i0_real	1.1040e+07
I(0) uncertainty (real space) i0_real_error	1.7450e+05
Rg (reciprocal space) rg_reciprocal	21.37 Å
I(0) (reciprocal space) i0_reciprocal	11040000.0000
Solution quality estimate total_estimate	0.7774
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.3 Å
Skewness Skewness skewness	0.715
Kurtosis Kurtosis kurtosis	0.351
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1742000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.530; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.582; Smooth: 0.929

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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	Bone morphogenetic protein 6
Molecular weight formula_weight	13287.5 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	1810

MAQAKHKQRKRLKACRKHELYVSFQDLGWQDWIIAPKGYAANYCDGECSFPLNAHMNATNHAIVQTLVHLMNPEYVPKPCCAPTKLNAISVLYFDDNSNVILKKYRNMVVRACGCH

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 BL21(DE3)

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	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	78

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2r53a_
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.17.1.2 — Transforming growth factor (TGF)-beta

Domain ID domain_id	d2r53b_
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.17.1.2 — Transforming growth factor (TGF)-beta

CATH v4.4 (2 domains)

Domain ID domain_id	2r53A00
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	2r53B00
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	99.780 Å
Unit-cell length b length_b	99.780 Å
Unit-cell length c length_c	86.760 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 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2610
R_work r_work	0.2590
R_free r_free	0.2790

fit	/app/data/saxs_computation/r5/2r53/2r53.fit
pddf	/app/data/pr_computation/r5/2r53/2r53.pr.out
profile	/app/data/saxs_computation/r5/2r53/2r53.dat

Crystal structure analysis of Bone Morphogenetic Protein-6 variant B2 (B2-BMP-6)

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

Bone morphogenetic protein 6

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