8daa

Coevolved affibody-Z domain pair LL2.c7

Method: X-RAY DIFFRACTION Dmax: 88.1 Å Quality: REASONABLE

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

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 213–269 Mutation:Q9L, F13V, G29A, I31F Affibody LL2.FIVK × 1 MLI MALONATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;295 K;3.0 M Ammonium sulfate, 100 mM HEPES pH 7.0 cryoprotected with sodium malonate Resolution 1.75 Å R-free 0.298
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 213–269 Mutation:Q9L, F13V, G29A, I31F Affibody LL2.FIVK × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;295 K;3.0 M Ammonium sulfate, 100 mM HEPES pH 7.0 cryoprotected with sodium malonate Resolution 1.75 Å R-free 0.298

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 3–59; UniProt 213–269 Author chain C; PDBConstruct 3–59; UniProt 213–269

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 8daa

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8daa
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8daa
Deposition date deposition_date2022-06-13
Structure title titleCoevolved affibody-Z domain pair LL2.c7
Keywords keywordsaffibody, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.29
Radius of gyration Rg (electron density) rg_electron25.85
Forward intensity I(0) i010559500.00
Molecular weight molecular_weight24279.0 kDa
Excluded volume excluded_volume30139 ų
Envelope volume envelope_volume40539 ų
Hydration-shell volume shell_volume14022 ų
Envelope diameter envelope_diameter91.2
Shell Rg shell_rg31.37
Envelope Rg envelope_rg25.61
Shape Rg shape_rg25.85
Total Rg total_rg26.52
Total atoms total_atoms1718
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 dmax88.1
Rg (real space) rg_real26.60
Rg uncertainty (real space) rg_real_error0.92
I(0) (real space) i0_real1.0560e+07
I(0) uncertainty (real space) i0_real_error1.6910e+05
Rg (reciprocal space) rg_reciprocal26.51
I(0) (reciprocal space) i0_reciprocal10560000.0000
Solution quality estimate total_estimate0.7496
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary19.1
Skewness Skewness skewness0.401
Kurtosis Kurtosis kurtosis-0.796
Angular range angular_range— – 0.3000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1228000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.496; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.277; Smooth: 0.975

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id8daaA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily420 — Immunoglobulin FC, subunit C
Domain ID domain_id8daaB01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily420 — Immunoglobulin FC, subunit C
Domain ID domain_id8daaC01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily420 — Immunoglobulin FC, subunit C
Domain ID domain_id8daaD01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily420 — Immunoglobulin FC, subunit C

8. Citations (1)

9. Files and Curves (10)