3mya

Crystal Structure of HP67 H41F - P61

Method: X-RAY DIFFRACTION Dmax: 55.6 Å Quality: GOOD

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

Villin-1

Gallus gallus

UniProt P02640

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 760–826 Fragment:Villin Headpiece (unp residues 760-826) Mutation:H41F No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;0.2 M Ammonium Sulfate, 0.1 M 2-morpholinoethanesulfonic Acid, 30% Polyethylene Glycol 8,000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.50 Å R-free 0.277
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 760–826 Fragment:Villin Headpiece (unp residues 760-826) Mutation:H41F No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;0.2 M Ammonium Sulfate, 0.1 M 2-morpholinoethanesulfonic Acid, 30% Polyethylene Glycol 8,000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.50 Å R-free 0.277

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.

45 other PDB entries and 50 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VILI_CHICK
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–67; UniProt 760–826 Author chain B; PDBConstruct 1–67; UniProt 760–826

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 3mya

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3mya
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3mya
Deposition date deposition_date2010-05-10
Structure title titleCrystal Structure of HP67 H41F - P61
Keywords keywordsvillin headpiece, alpha helix, protein, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier16.79
Radius of gyration Rg (electron density) rg_electron15.78
Forward intensity I(0) i04096830.00
Molecular weight molecular_weight14894.0 kDa
Excluded volume excluded_volume18869 ų
Envelope volume envelope_volume22164 ų
Hydration-shell volume shell_volume12417 ų
Envelope diameter envelope_diameter55.7
Shell Rg shell_rg20.87
Envelope Rg envelope_rg16.03
Shape Rg shape_rg15.75
Total Rg total_rg16.89
Total atoms total_atoms1053
Residues n_residues131
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 dmax55.6
Rg (real space) rg_real16.78
Rg uncertainty (real space) rg_real_error0.38
I(0) (real space) i0_real4.0970e+06
I(0) uncertainty (real space) i0_real_error4.7680e+04
Rg (reciprocal space) rg_reciprocal16.78
I(0) (reciprocal space) i0_reciprocal4097000.0000
Solution quality estimate total_estimate0.7920
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary54.9
Skewness Skewness skewness0.329
Kurtosis Kurtosis kurtosis-0.293
Angular range angular_range— – 0.4750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1037000.0000
Real-space data points n_real_points78
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.767; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3myaa_
Class classa — All alpha proteins
Fold Fold folda.14 — VHP, Villin headpiece domain
Superfamily Superfamily superfamilya.14.1 — VHP, Villin headpiece domain
Family Family familya.14.1.1 — VHP, Villin headpiece domain
Domain ID domain_idd3myab_
Class classa — All alpha proteins
Fold Fold folda.14 — VHP, Villin headpiece domain
Superfamily Superfamily superfamilya.14.1 — VHP, Villin headpiece domain
Family Family familya.14.1.1 — VHP, Villin headpiece domain

CATH v4.4 (2 domains)

Domain ID domain_id3myaA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology950 — Villin Headpiece Domain; Chain A
Homologous superfamily homologous superfamily10 — Villin headpiece domain
Domain ID domain_id3myaB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology950 — Villin Headpiece Domain; Chain A
Homologous superfamily homologous superfamily10 — Villin headpiece domain

8. Citations (1)

9. Files and Curves (10)