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2mbk

The Clip-segment of the von Willebrand domain 1 of the BMP modulator protein Crossveinless 2 is preformed

Method: SOLUTION NMR Dmax: 60.0 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Crossveinless 2

Danio rerio

UniProt Q5D734

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 28–93 Fragment：UNP residues 28-93 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.6；300 K；Ionic strength (raw mmCIF value) 0.04；Pressure ambient NMR sample composition：2 mM [U-99% 13C; U-99% 15N] CV2 VWC1, 20 mM sodium phosphate, 20 mM sodium chloride, 5 % [U-2H] D2O, 0.2 % sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O NMR sample composition：1.5 mM [U-99% 15N] CV2 VWC1, 20 mM sodium phosphate, 20 mM sodium chloride, 5 % [U-2H] D2O, 0.2 % sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O NMR sample composition：2 mM CV2 VWC1, 20 mM sodium phosphate, 20 mM sodium chloride, 5 % [U-2H] D2O, 0.2 % sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O Resolution not provided

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 2MBK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3BK3 Crystal structure of the complex of BMP-2 and the first Von Willebrand domain type C of Crossveinless-2 Deposited 2007-12-05 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 28–93（66 aa） Fragment：VWC1 CV-2, VWC domain 1, UNP residues 28-93
Chain D 28–93（66 aa） Fragment：VWC1 CV-2, VWC domain 1, UNP residues 28-93
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；2.2M ammonium phosphate, 0.1M Tris pH 7.5, 8% glycerol, 5% sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.70 Å R-free 0.245
3BK3 Crystal structure of the complex of BMP-2 and the first Von Willebrand domain type C of Crossveinless-2 Deposited 2007-12-05 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 28–93（66 aa） Fragment：VWC1 CV-2, VWC domain 1, UNP residues 28-93
Chain D 28–93（66 aa） Fragment：VWC1 CV-2, VWC domain 1, UNP residues 28-93
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；2.2M ammonium phosphate, 0.1M Tris pH 7.5, 8% glycerol, 5% sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.70 Å R-free 0.245
3BK3 Crystal structure of the complex of BMP-2 and the first Von Willebrand domain type C of Crossveinless-2 Deposited 2007-12-05 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 28–93（66 aa） Fragment：VWC1 CV-2, VWC domain 1, UNP residues 28-93
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；2.2M ammonium phosphate, 0.1M Tris pH 7.5, 8% glycerol, 5% sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.70 Å R-free 0.245
3BK3 Crystal structure of the complex of BMP-2 and the first Von Willebrand domain type C of Crossveinless-2 Deposited 2007-12-05 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 28–93（66 aa） Fragment：VWC1 CV-2, VWC domain 1, UNP residues 28-93
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；2.2M ammonium phosphate, 0.1M Tris pH 7.5, 8% glycerol, 5% sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.70 Å R-free 0.245

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

View Construct and Data Evidence
UniProt name Q5D734_DANRE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–69； UniProt 28–93

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 2mbk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2mbk
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2mbk
Deposition date deposition_date2013-08-02
Structure title titleThe Clip-segment of the von Willebrand domain 1 of the BMP modulator protein Crossveinless 2 is preformed
Keywords keywordsvon Willebrand type C domain, BMP modulator, Crossveinless 2, BMPER, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.25 Å
Radius of gyration Rg (electron density) rg_electron15.61 Å
Forward intensity I(0) i088702100.00
Molecular weight molecular_weight71813.0 kDa
Excluded volume excluded_volume87534 ų
Envelope volume envelope_volume26475 ų
Hydration-shell volume shell_volume12820 ų
Envelope diameter envelope_diameter61.7 Å
Shell Rg shell_rg23.19 Å
Envelope Rg envelope_rg18.90 Å
Shape Rg shape_rg15.64 Å
Total Rg total_rg15.88 Å
Total atoms total_atoms9680
Residues n_residues669
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax60.0 Å
Rg (real space) rg_real15.47 Å
Rg uncertainty (real space) rg_real_error0.66 Å
I(0) (real space) i0_real8.8700e+07
I(0) uncertainty (real space) i0_real_error1.1520e+06
Rg (reciprocal space) rg_reciprocal15.46 Å
I(0) (reciprocal space) i0_reciprocal88700000.0000
Solution quality estimate total_estimate0.6852
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary15.2 Å
Skewness Skewness skewness0.526
Kurtosis Kurtosis kurtosis-0.315
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha112100.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.574; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.180; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2mbkA00
Class class6 — Special
Architecture architecture20 — Other non-globular
Topology topology200 — Defensin A-like
Homologous superfamily homologous superfamily20 —
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8. Citations (1)

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9. Files and Curves (10)