9dpq

BMP-9 Wild-Type Dimer without Radiation Damage in Acidic pH

Method: X-RAY DIFFRACTION Dmax: 69.3 Å Quality: GOOD

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

Growth/differentiation factor 2

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 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 320–429 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

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.

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 1
Chains and sequence ranges Author chain A; 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.

SAXS scattering curve SAXS Profile

SAXS profile for 9dpq

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9dpq
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9dpq
Deposition date deposition_date2024-09-23
最后修订 last_revision2025-03-05
Structure title titleBMP-9 Wild-Type Dimer without Radiation Damage in Acidic pH
Keywords keywordsSIGNALING PROTEIN, BMP, bone morphogenetic protein, TGF-beta family; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier18.40
Radius of gyration Rg (electron density) rg_electron18.47
Forward intensity I(0) i02980170.00
Molecular weight molecular_weight12477.0 kDa
Excluded volume excluded_volume15584 ų
Envelope volume envelope_volume19572 ų
Hydration-shell volume shell_volume10011 ų
Envelope diameter envelope_diameter68.2
Shell Rg shell_rg22.32
Envelope Rg envelope_rg18.66
Shape Rg shape_rg18.47
Total Rg total_rg19.19
Total atoms total_atoms1677
Residues n_residues106
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax69.3
Rg (real space) rg_real18.58
Rg uncertainty (real space) rg_real_error0.77
I(0) (real space) i0_real2.9800e+06
I(0) uncertainty (real space) i0_real_error3.9860e+04
Rg (reciprocal space) rg_reciprocal18.56
I(0) (reciprocal space) i0_reciprocal2980000.0000
Solution quality estimate total_estimate0.7787
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary16.1
Skewness Skewness skewness0.475
Kurtosis Kurtosis kurtosis-0.442
Angular range angular_range— – 0.4300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha294800.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.595; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.337; Smooth: 0.997

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)