4dat

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

Method: X-RAY DIFFRACTION Dmax: 64.0 Å Quality: REASONABLE

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) MG MAGNESIUM ION × 2 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 1.40 Å R-free 0.183

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 441–449 Fragment:14-3-3 binding motif II (UNP residues 441-449) Non-standard monomer:Yes (specific site not provided by mmCIF) 14-3-3 protein sigma × 2 (P31947) MG MAGNESIUM ION × 2 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 1.40 Å R-free 0.183

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 1–9; UniProt 441–449

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 4dat

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id4dat
Deposition date deposition_date2012-01-13
Structure title titleStructure of 14-3-3 sigma in complex with PADI6 14-3-3 binding motif II
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_guinier19.38
Radius of gyration Rg (electron density) rg_electron18.30
Forward intensity I(0) i012142100.00
Molecular weight molecular_weight25560.0 kDa
Excluded volume excluded_volume31821 ų
Envelope volume envelope_volume37556 ų
Hydration-shell volume shell_volume17481 ų
Envelope diameter envelope_diameter66.2
Shell Rg shell_rg24.22
Envelope Rg envelope_rg18.58
Shape Rg shape_rg18.28
Total Rg total_rg19.24
Total atoms total_atoms1792
Residues n_residues225
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 dmax64.0
Rg (real space) rg_real19.30
Rg uncertainty (real space) rg_real_error0.40
I(0) (real space) i0_real1.2140e+07
I(0) uncertainty (real space) i0_real_error1.6690e+05
Rg (reciprocal space) rg_reciprocal19.31
I(0) (reciprocal space) i0_reciprocal12140000.0000
Solution quality estimate total_estimate0.6589
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary57.7
Skewness Skewness skewness0.211
Kurtosis Kurtosis kurtosis-0.353
Angular range angular_range— – 0.4100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2523000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.834; Stabil: 1.000; Sysdev: 0.356; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id4datA00
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)