5xby

Crystal structure of the PKA-Protein A fusion protein (end-to-end fusion)

Method: X-RAY DIFFRACTION Dmax: 96.0 Å Quality: GOOD

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

cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A

Staphylococcus aureus

UniProt P13861

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 5–44 Chain B; UniProt 5–44 Fragment:UNP RESIDUES 5-44,UNP RESIDUES 217-269 Mutation:G240A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 8.5;296 K;100mM Tris pH 8.5, 2.16M Sodium formate Resolution 3.25 Å R-free 0.307
2 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 5–44 Chain D; UniProt 5–44 Fragment:UNP RESIDUES 5-44,UNP RESIDUES 217-269 Mutation:G240A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 8.5;296 K;100mM Tris pH 8.5, 2.16M Sodium formate Resolution 3.25 Å R-free 0.307

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.

7 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KAP2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 5–44; UniProt 5–44 Author chain B; PDBConstruct 5–44; UniProt 5–44 Author chain C; PDBConstruct 5–44; UniProt 5–44 Author chain D; PDBConstruct 5–44; UniProt 5–44

cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A

Staphylococcus aureus

UniProt P38507

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 217–269 Chain B; UniProt 217–269 Fragment:UNP RESIDUES 5-44,UNP RESIDUES 217-269 Mutation:G240A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 8.5;296 K;100mM Tris pH 8.5, 2.16M Sodium formate Resolution 3.25 Å R-free 0.307
2 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 217–269 Chain D; UniProt 217–269 Fragment:UNP RESIDUES 5-44,UNP RESIDUES 217-269 Mutation:G240A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 8.5;296 K;100mM Tris pH 8.5, 2.16M Sodium formate Resolution 3.25 Å R-free 0.307

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.

66 other PDB entries and 126 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPA_STAAU
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 45–97; UniProt 217–269 Author chain B; PDBConstruct 45–97; UniProt 217–269 Author chain C; PDBConstruct 45–97; UniProt 217–269 Author chain D; PDBConstruct 45–97; UniProt 217–269

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 5xby

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5xby
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5xby
Deposition date deposition_date2017-03-21
Structure title titleCrystal structure of the PKA-Protein A fusion protein (end-to-end fusion)
Keywords keywordssynthetic protein, kinase, LYASE, SIGNALING PROTEIN, PROTEIN BINDING; 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_guinier29.05
Radius of gyration Rg (electron density) rg_electron28.16
Forward intensity I(0) i021999500.00
Molecular weight molecular_weight36044.0 kDa
Excluded volume excluded_volume45192 ų
Envelope volume envelope_volume62194 ų
Hydration-shell volume shell_volume20937 ų
Envelope diameter envelope_diameter101.1
Shell Rg shell_rg31.36
Envelope Rg envelope_rg28.10
Shape Rg shape_rg28.16
Total Rg total_rg28.55
Total atoms total_atoms2553
Residues n_residues313
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 dmax96.0
Rg (real space) rg_real29.13
Rg uncertainty (real space) rg_real_error0.81
I(0) (real space) i0_real2.2000e+07
I(0) uncertainty (real space) i0_real_error3.0130e+05
Rg (reciprocal space) rg_reciprocal29.10
I(0) (reciprocal space) i0_reciprocal22000000.0000
Solution quality estimate total_estimate0.8669
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary41.9
Skewness Skewness skewness0.288
Kurtosis Kurtosis kurtosis-0.463
Angular range angular_range— – 0.2750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2164000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.871; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.796; Smooth: 0.856

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

8. Citations (1)

9. Files and Curves (10)