5w5m

Crystal structure of human IgG4-Sigma1 Fc fragment

Method: X-RAY DIFFRACTION Dmax: 79.0 Å Quality: EXCELLENT

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

Immunoglobulin heavy constant gamma 4

Homo sapiens

UniProt P01861

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Homooligomer Protein × 2 其他Polymer 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 106–327 Chain B; UniProt 106–327 Fragment:Sigma1 Fc fragment, UNP residues 106-327 ;beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 GOL GLYCEROL × 2 ACT ACETATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;9% (w/v) PEG 20K, 0.1 M sodium acetate, pH 5.5 Resolution 1.90 Å R-free 0.225

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.

13 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IGHG4_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–223; UniProt 106–327 Author chain B; PDBConstruct 2–223; UniProt 106–327

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 5w5m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5w5m
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5w5m
Deposition date deposition_date2017-06-15
Structure title titleCrystal structure of human IgG4-Sigma1 Fc fragment
Keywords keywordsFC, IMMUNOGLOBULIN FOLD, 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_guinier26.33
Radius of gyration Rg (electron density) rg_electron25.10
Forward intensity I(0) i042827700.00
Molecular weight molecular_weight50235.0 kDa
Excluded volume excluded_volume62699 ų
Envelope volume envelope_volume79923 ų
Hydration-shell volume shell_volume26509 ų
Envelope diameter envelope_diameter79.5
Shell Rg shell_rg32.32
Envelope Rg envelope_rg24.64
Shape Rg shape_rg25.10
Total Rg total_rg25.93
Total atoms total_atoms3532
Residues n_residues416
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 dmax79.0
Rg (real space) rg_real26.18
Rg uncertainty (real space) rg_real_error0.40
I(0) (real space) i0_real4.2830e+07
I(0) uncertainty (real space) i0_real_error5.0850e+05
Rg (reciprocal space) rg_reciprocal26.23
I(0) (reciprocal space) i0_reciprocal42830000.0000
Solution quality estimate total_estimate0.9158
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.9
Skewness Skewness skewness0.039
Kurtosis Kurtosis kurtosis-0.658
Angular range angular_range— – 0.3000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6345000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.972; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.986

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id5w5mA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5w5mB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)