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2ibb

Crystal Structure of the First and Second FNIII Domains of Ihog

Method: X-RAY DIFFRACTION Dmax: 74.7 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CG9211-PA

Drosophila melanogaster

UniProt Q9VM64

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 466–676 Fragment：Extracellular FNIII Domains SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.9；293 K；0.05M Tris-HCl pH 7.9, 23% PEG 3350, 0.2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.40 Å R-free 0.275

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 2IBB Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2IBG Crystal Structure of Hedgehog Bound to the FNIII Domains of Ihog Deposited 2006-09-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 466–677（212 aa） Fragment：Extracellular FNIII Domains
Not recorded PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；2.0M Na/K phosphate pH 6.4, 0.2M lithium sulfate, 0.05M CAPS pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.246
2IBG Crystal Structure of Hedgehog Bound to the FNIII Domains of Ihog Deposited 2006-09-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 466–677（212 aa） Fragment：Extracellular FNIII Domains
Not recorded PO4 PHOSPHATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；2.0M Na/K phosphate pH 6.4, 0.2M lithium sulfate, 0.05M CAPS pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.246
2IBG Crystal Structure of Hedgehog Bound to the FNIII Domains of Ihog Deposited 2006-09-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 466–677（212 aa） Fragment：Extracellular FNIII Domains
Not recorded PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；2.0M Na/K phosphate pH 6.4, 0.2M lithium sulfate, 0.05M CAPS pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.246
2IBG Crystal Structure of Hedgehog Bound to the FNIII Domains of Ihog Deposited 2006-09-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 466–677（212 aa） Fragment：Extracellular FNIII Domains
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；2.0M Na/K phosphate pH 6.4, 0.2M lithium sulfate, 0.05M CAPS pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.246

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

View Construct and Data Evidence
UniProt name Q9VM64_DROME
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–213； UniProt 466–676

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 2ibb

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2ibb
Deposition date deposition_date2006-09-11
Structure title titleCrystal Structure of the First and Second FNIII Domains of Ihog
Keywords keywordsihog, hedgehog, fibronectin type III, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier19.12 Å
Radius of gyration Rg (electron density) rg_electron17.84 Å
Forward intensity I(0) i010440400.00
Molecular weight molecular_weight23909.0 kDa
Excluded volume excluded_volume29877 ų
Envelope volume envelope_volume34694 ų
Hydration-shell volume shell_volume16543 ų
Envelope diameter envelope_diameter66.0 Å
Shell Rg shell_rg23.49 Å
Envelope Rg envelope_rg18.05 Å
Shape Rg shape_rg17.78 Å
Total Rg total_rg18.91 Å
Total atoms total_atoms1685
Residues n_residues208
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 dmax74.7 Å
Rg (real space) rg_real19.04 Å
Rg uncertainty (real space) rg_real_error0.83 Å
I(0) (real space) i0_real1.0440e+07
I(0) uncertainty (real space) i0_real_error1.5600e+05
Rg (reciprocal space) rg_reciprocal19.05 Å
I(0) (reciprocal space) i0_reciprocal10440000.0000
Solution quality estimate total_estimate0.6800
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks4
Primary peak position r_peak_primary19.7 Å
Skewness Skewness skewness0.184
Kurtosis Kurtosis kurtosis-0.414
Angular range angular_range— – 0.4150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2220000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.401; Stabil: 0.936; Sysdev: 1.000; Positv: 1.000; Valcen: 0.825; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd2ibba1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.2 — Fibronectin type III
Family Family familyb.1.2.1 — Fibronectin type III
Domain ID domain_idd2ibba2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.2 — Fibronectin type III
Family Family familyb.1.2.1 — Fibronectin type III
Domain ID domain_idd2ibba3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id2ibbA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2ibbA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (1)

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9. Files and Curves (10)