4dau

Structure of 14-3-3 sigma in complex with PADI6 14-3-3 binding motif I

Method: X-RAY DIFFRACTION Dmax: 63.2 Å Quality: GOOD

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

14-3-3 protein sigma

Homo sapiens

UniProt P31947

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–231 Fragment:UNP residues 1-231 Peptidylarginine Deiminase type VI × 2 (Q330K5) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;277 K;26.6% v/v PEG400, 0.19 M calcium chloride, 5% v/v glycerol, 0.095 M HEPES sodium, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.00 Å R-free 0.228

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.

523 other PDB entries and 543 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 1433S_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–234; UniProt 1–231

Peptidylarginine Deiminase type VI

OrganismNot specified

UniProt Q330K5

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 1–13 Fragment:14-3-3 binding motif I (UNP residues 1-13) Non-standard monomer:Yes (specific site not provided by mmCIF) 14-3-3 protein sigma × 2 (P31947) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;277 K;26.6% v/v PEG400, 0.19 M calcium chloride, 5% v/v glycerol, 0.095 M HEPES sodium, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.00 Å R-free 0.228

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.

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

View Construct and Data Evidence
UniProt name Q330K5_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–13; UniProt 1–13

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 4dau

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4dau
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4dau
Deposition date deposition_date2012-01-13
Structure title titleStructure of 14-3-3 sigma in complex with PADI6 14-3-3 binding motif I
Keywords keywords14-3-3 fold, protein-protein interaction, SIGNALING PROTEIN-PROTEIN BINDING complex; SIGNALING PROTEIN/PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier19.03
Radius of gyration Rg (electron density) rg_electron17.97
Forward intensity I(0) i012268300.00
Molecular weight molecular_weight25684.0 kDa
Excluded volume excluded_volume31971 ų
Envelope volume envelope_volume36620 ų
Hydration-shell volume shell_volume17247 ų
Envelope diameter envelope_diameter65.3
Shell Rg shell_rg23.94
Envelope Rg envelope_rg18.41
Shape Rg shape_rg17.96
Total Rg total_rg18.88
Total atoms total_atoms1798
Residues n_residues226
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 dmax63.2
Rg (real space) rg_real18.96
Rg uncertainty (real space) rg_real_error0.50
I(0) (real space) i0_real1.2270e+07
I(0) uncertainty (real space) i0_real_error1.5620e+05
Rg (reciprocal space) rg_reciprocal18.97
I(0) (reciprocal space) i0_reciprocal12270000.0000
Solution quality estimate total_estimate0.8054
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary23.7
Skewness Skewness skewness0.226
Kurtosis Kurtosis kurtosis-0.337
Angular range angular_range— – 0.4200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2581000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.824; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id4dauA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology190 — Delta-Endotoxin; domain 1
Homologous superfamily homologous superfamily20 — 14-3-3 domain

8. Citations (1)

9. Files and Curves (10)