5h76

Crystal structure of the DARPin-Protein A fusion protein

Method: X-RAY DIFFRACTION Dmax: 90.3 Å Quality: EXCELLENT

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

DARPin,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 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 235–267 Fragment:RESIDUES 9-176,177-209 (UNP RESIDUES 235-267) Mutation:G182A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 9.5;296 K;0.63M sodium potassium phosphate pH 9.5 Resolution 2.60 Å R-free 0.250
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 235–267 Fragment:RESIDUES 9-176,177-209 (UNP RESIDUES 235-267) Mutation:G182A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 9.5;296 K;0.63M sodium potassium phosphate pH 9.5 Resolution 2.60 Å R-free 0.250
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 235–267 Fragment:RESIDUES 9-176,177-209 (UNP RESIDUES 235-267) Mutation:G182A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 9.5;296 K;0.63M sodium potassium phosphate pH 9.5 Resolution 2.60 Å R-free 0.250

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 125 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 169–201; UniProt 235–267 Author chain B; PDBConstruct 169–201; UniProt 235–267 Author chain C; PDBConstruct 169–201; UniProt 235–267

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 5h76

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5h76
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5h76
Deposition date deposition_date2016-11-17
Structure title titleCrystal structure of the DARPin-Protein A fusion protein
Keywords keywordssynthetic protein, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.59
Radius of gyration Rg (electron density) rg_electron28.57
Forward intensity I(0) i067895800.00
Molecular weight molecular_weight63909.0 kDa
Excluded volume excluded_volume79731 ų
Envelope volume envelope_volume102620 ų
Hydration-shell volume shell_volume30688 ų
Envelope diameter envelope_diameter94.1
Shell Rg shell_rg35.29
Envelope Rg envelope_rg28.47
Shape Rg shape_rg28.55
Total Rg total_rg29.30
Total atoms total_atoms4512
Residues n_residues591
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 dmax90.3
Rg (real space) rg_real29.50
Rg uncertainty (real space) rg_real_error0.64
I(0) (real space) i0_real6.7900e+07
I(0) uncertainty (real space) i0_real_error9.0490e+05
Rg (reciprocal space) rg_reciprocal29.54
I(0) (reciprocal space) i0_reciprocal67900000.0000
Solution quality estimate total_estimate0.9111
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.1
Skewness Skewness skewness0.169
Kurtosis Kurtosis kurtosis-0.589
Angular range angular_range— – 0.2700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5431000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.979; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.904

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

8. Citations (1)

9. Files and Curves (10)