4c54

Crystal structure of recombinant human IgG4 Fc

Method: X-RAY DIFFRACTION Dmax: 79.4 Å Quality: EXCELLENT

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

IG GAMMA-4 CHAIN C REGION

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 114–327 Chain B; UniProt 114–327 Fragment:FC FRAGMENT, RESIDUES 114-327 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]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 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 EDO 1,2-ETHANEDIOL × 9 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;MES PH6.5. 18-20% PEG 20 000 Resolution 1.90 Å R-free 0.209

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 1–214; UniProt 114–327 Author chain B; PDBConstruct 1–214; UniProt 114–327

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 4c54

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4c54
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4c54
Deposition date deposition_date2013-09-10
Structure title titleCrystal structure of recombinant human IgG4 Fc
Keywords keywordsIMMUNE SYSTEM, IMMUNOGLOBULIN, IGG1; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.48
Radius of gyration Rg (electron density) rg_electron25.22
Forward intensity I(0) i043315900.00
Molecular weight molecular_weight50629.0 kDa
Excluded volume excluded_volume63150 ų
Envelope volume envelope_volume81512 ų
Hydration-shell volume shell_volume26833 ų
Envelope diameter envelope_diameter80.1
Shell Rg shell_rg32.61
Envelope Rg envelope_rg24.80
Shape Rg shape_rg25.23
Total Rg total_rg26.03
Total atoms total_atoms3557
Residues n_residues419
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 dmax79.4
Rg (real space) rg_real26.33
Rg uncertainty (real space) rg_real_error0.52
I(0) (real space) i0_real4.3320e+07
I(0) uncertainty (real space) i0_real_error5.6460e+05
Rg (reciprocal space) rg_reciprocal26.38
I(0) (reciprocal space) i0_reciprocal43320000.0000
Solution quality estimate total_estimate0.9149
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.1
Skewness Skewness skewness0.044
Kurtosis Kurtosis kurtosis-0.659
Angular range angular_range— – 0.3000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7260000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.970; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.985

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id4c54A01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4c54A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4c54B01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4c54B02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)