SAXSdb — 1lxi

▼

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

BONE MORPHOGENETIC PROTEIN 7

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 293–431	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.5；277 K；20% MPD, 0.1M Sodium Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.244

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 1LXI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BMP BONE MORPHOGENETIC PROTEIN-7 Deposited 1995-12-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 293–431（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å R-free 0.308
1LX5 Crystal Structure of the BMP7/ActRII Extracellular Domain Complex Deposited 2002-06-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 293–431（139 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；296 K；1M sodium acetate, 0.1M imidazole, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 3.30 Å R-free 0.279
1M4U Crystal structure of Bone Morphogenetic Protein-7 (BMP-7) in complex with the secreted antagonist Noggin Deposited 2002-07-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain L 293–431（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.6 M disodium, 1.0 M monopotassium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.42 Å R-free 0.273

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BMP7_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–139； UniProt 293–431

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1lxi
Deposition date deposition_date	2002-06-05
Structure title title	Refinement of BMP7 crystal structure
Keywords keywords	Cystine-knot growth factor, HORMONE-GROWTH FACTOR COMPLEX; HORMONE/GROWTH FACTOR
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	19.08 Å
Radius of gyration Rg (electron density) rg_electron	19.18 Å
Forward intensity I(0) i0	2847390.00
Molecular weight molecular_weight	12010.0 kDa
Excluded volume excluded_volume	14982 Å³
Envelope volume envelope_volume	19152 Å³
Hydration-shell volume shell_volume	9668 Å³
Envelope diameter envelope_diameter	67.2 Å
Shell Rg shell_rg	22.45 Å
Envelope Rg envelope_rg	19.39 Å
Shape Rg shape_rg	19.25 Å
Total Rg total_rg	19.55 Å
Total atoms total_atoms	842
Residues n_residues	104
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	69.5 Å
Rg (real space) rg_real	19.39 Å
Rg uncertainty (real space) rg_real_error	0.79 Å
I(0) (real space) i0_real	2.8470e+06
I(0) uncertainty (real space) i0_real_error	3.9800e+04
Rg (reciprocal space) rg_reciprocal	19.34 Å
I(0) (reciprocal space) i0_reciprocal	2847000.0000
Solution quality estimate total_estimate	0.7692
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.4 Å
Skewness Skewness skewness	0.551
Kurtosis Kurtosis kurtosis	-0.422
Angular range angular_range	— – 0.4150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	291300.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.592; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.221; Smooth: 0.999

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	BONE MORPHOGENETIC PROTEIN 7
Molecular weight formula_weight	15699.7 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	920

STGSKQRSQNRSKTPKNQEALRMANVAENSSSDQRQACKKHELYVSFRDLGWQDWIIAPEGYAAYYCEGECAFPLNSYMNATNHAIVQTLVHFINPETVPKPCCAPTQLNAISVLYFDDSSNVILKKYRNMVVRACGCH

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 2 Entity 2 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	71

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1lxia_
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 (1 domains)

Domain ID domain_id	1lxiA00
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

▶

8. Citations (1)

▶

Unit-cell length a length_a	101.294 Å
Unit-cell length b length_b	101.294 Å
Unit-cell length c length_c	41.812 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	6

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	23.960 Å
R factor r_factor	0.2287
R_work r_work	0.2279
R_free r_free	0.2445

fit	/app/data/saxs_computation/lx/1lxi/1lxi.fit
pddf	/app/data/pr_computation/lx/1lxi/1lxi.pr.out
profile	/app/data/saxs_computation/lx/1lxi/1lxi.dat

Refinement of BMP7 crystal structure

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

BONE MORPHOGENETIC PROTEIN 7

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