4wwi

Crystal structure of the C domain of staphylococcal protein A in complex with the Fc fragment of human IgG at 2.3 Angstrom resolution

Method: X-RAY DIFFRACTION Dmax: 104.8 Å Quality: EXCELLENT

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 270–327 Fragment:UNP residues 270-327 Ig gamma-3 chain C region × 1 (P01860) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;298 K;NaOAc, ammonium sulfate, PEG 5K MME, glycerol Resolution 2.31 Å R-free 0.251
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 270–327 Fragment:UNP residues 270-327 Ig gamma-3 chain C region × 1 (P01860) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;298 K;NaOAc, ammonium sulfate, PEG 5K MME, glycerol Resolution 2.31 Å R-free 0.251
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 270–327 Fragment:UNP residues 270-327 Ig gamma-3 chain C region × 1 (P01860) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;298 K;NaOAc, ammonium sulfate, PEG 5K MME, glycerol Resolution 2.31 Å R-free 0.251

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 1–58; UniProt 270–327 Author chain B; PDBConstruct 1–58; UniProt 270–327 Author chain C; PDBConstruct 1–58; UniProt 270–327

Ig gamma-3 chain C region

Homo sapiens

UniProt P01860

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 D; UniProt 168–377 Fragment:UNP residues 168-377 Immunoglobulin G-binding protein A × 1 (P38507) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;298 K;NaOAc, ammonium sulfate, PEG 5K MME, glycerol Resolution 2.31 Å R-free 0.251
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 168–377 Fragment:UNP residues 168-377 Immunoglobulin G-binding protein A × 1 (P38507) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;298 K;NaOAc, ammonium sulfate, PEG 5K MME, glycerol Resolution 2.31 Å R-free 0.251
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain F; UniProt 168–377 Fragment:UNP residues 168-377 Immunoglobulin G-binding protein A × 1 (P38507) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;298 K;NaOAc, ammonium sulfate, PEG 5K MME, glycerol Resolution 2.31 Å R-free 0.251

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.

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

View Construct and Data Evidence
UniProt name IGHG3_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain D; PDBConstruct 1–210; UniProt 168–377 Author chain E; PDBConstruct 1–210; UniProt 168–377 Author chain F; PDBConstruct 1–210; UniProt 168–377

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 4wwi

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id4wwi
Deposition date deposition_date2014-11-11
Structure title titleCrystal structure of the C domain of staphylococcal protein A in complex with the Fc fragment of human IgG at 2.3 Angstrom resolution
Keywords keywordsthree-helix bundle, conformational heterogeneity, S. aureus, antibody binding, 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_guinier32.99
Radius of gyration Rg (electron density) rg_electron32.13
Forward intensity I(0) i0117745000.00
Molecular weight molecular_weight86198.0 kDa
Excluded volume excluded_volume108070 ų
Envelope volume envelope_volume149050 ų
Hydration-shell volume shell_volume38946 ų
Envelope diameter envelope_diameter111.1
Shell Rg shell_rg38.75
Envelope Rg envelope_rg31.73
Shape Rg shape_rg32.11
Total Rg total_rg32.78
Total atoms total_atoms12057
Residues n_residues755
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 dmax104.8
Rg (real space) rg_real32.84
Rg uncertainty (real space) rg_real_error0.70
I(0) (real space) i0_real1.1770e+08
I(0) uncertainty (real space) i0_real_error1.5030e+06
Rg (reciprocal space) rg_reciprocal32.91
I(0) (reciprocal space) i0_reciprocal117800000.0000
Solution quality estimate total_estimate0.9004
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary41.5
Skewness Skewness skewness0.165
Kurtosis Kurtosis kurtosis-0.460
Angular range angular_range— – 0.2400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7778000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.947

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

Domain ID domain_idd4wwia_
Class classa — All alpha proteins
Fold Fold folda.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamilya.8.1 — Bacterial immunoglobulin/albumin-binding domains
Family Family familya.8.1.1 — Immunoglobulin-binding protein A modules
Domain ID domain_idd4wwib_
Class classa — All alpha proteins
Fold Fold folda.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamilya.8.1 — Bacterial immunoglobulin/albumin-binding domains
Family Family familya.8.1.1 — Immunoglobulin-binding protein A modules
Domain ID domain_idd4wwic_
Class classa — All alpha proteins
Fold Fold folda.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamilya.8.1 — Bacterial immunoglobulin/albumin-binding domains
Family Family familya.8.1.1 — Immunoglobulin-binding protein A modules
Domain ID domain_idd4wwid1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd4wwid2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd4wwie1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd4wwie2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd4wwif1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd4wwif2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches

CATH v4.4 (9 domains)

Domain ID domain_id4wwiA00
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_id4wwiB00
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_id4wwiC00
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_id4wwiD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4wwiD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4wwiE01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4wwiE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4wwiF01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4wwiF02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)