4gjx

Crystal structure of CD23 lectin domain mutant D258A

Method: X-RAY DIFFRACTION Dmax: 115.0 Å Quality: EXCELLENT

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

Low affinity immunoglobulin epsilon Fc receptor

Homo sapiens

UniProt P06734

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 156–298 Fragment:UNP residues 156-298 Mutation:D258A GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5;291 K;18% ethanol, 4% PEG 400, 0.1 M sodium acetate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K Resolution 2.80 Å R-free 0.251
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 156–298 Fragment:UNP residues 156-298 Mutation:D258A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5;291 K;18% ethanol, 4% PEG 400, 0.1 M sodium acetate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K Resolution 2.80 Å R-free 0.251
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 156–298 Fragment:UNP residues 156-298 Mutation:D258A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5;291 K;18% ethanol, 4% PEG 400, 0.1 M sodium acetate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K Resolution 2.80 Å R-free 0.251
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 156–298 Fragment:UNP residues 156-298 Mutation:D258A GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5;291 K;18% ethanol, 4% PEG 400, 0.1 M sodium acetate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K Resolution 2.80 Å R-free 0.251
5 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain E; UniProt 156–298 Fragment:UNP residues 156-298 Mutation:D258A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5;291 K;18% ethanol, 4% PEG 400, 0.1 M sodium acetate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K Resolution 2.80 Å R-free 0.251
6 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain F; UniProt 156–298 Fragment:UNP residues 156-298 Mutation:D258A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5;291 K;18% ethanol, 4% PEG 400, 0.1 M sodium acetate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K Resolution 2.80 Å R-free 0.251
7 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain G; UniProt 156–298 Fragment:UNP residues 156-298 Mutation:D258A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5;291 K;18% ethanol, 4% PEG 400, 0.1 M sodium acetate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K Resolution 2.80 Å R-free 0.251
8 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain H; UniProt 156–298 Fragment:UNP residues 156-298 Mutation:D258A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5;291 K;18% ethanol, 4% PEG 400, 0.1 M sodium acetate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K Resolution 2.80 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.

22 other PDB entries and 72 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FCER2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–143; UniProt 156–298 Author chain B; PDBConstruct 1–143; UniProt 156–298 Author chain C; PDBConstruct 1–143; UniProt 156–298 Author chain D; PDBConstruct 1–143; UniProt 156–298 Author chain E; PDBConstruct 1–143; UniProt 156–298 Author chain F; PDBConstruct 1–143; UniProt 156–298 Author chain G; PDBConstruct 1–143; UniProt 156–298 Author chain H; PDBConstruct 1–143; UniProt 156–298

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 4gjx

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id4gjx
Deposition date deposition_date2012-08-10
Structure title titleCrystal structure of CD23 lectin domain mutant D258A
Keywords keywordsReceptor, 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_guinier36.79
Radius of gyration Rg (electron density) rg_electron36.33
Forward intensity I(0) i0258281000.00
Molecular weight molecular_weight123070.0 kDa
Excluded volume excluded_volume150930 ų
Envelope volume envelope_volume212830 ų
Hydration-shell volume shell_volume49199 ų
Envelope diameter envelope_diameter125.2
Shell Rg shell_rg42.28
Envelope Rg envelope_rg35.79
Shape Rg shape_rg36.32
Total Rg total_rg36.79
Total atoms total_atoms8642
Residues n_residues1078
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 dmax115.0
Rg (real space) rg_real36.63
Rg uncertainty (real space) rg_real_error0.81
I(0) (real space) i0_real2.5830e+08
I(0) uncertainty (real space) i0_real_error4.1050e+06
Rg (reciprocal space) rg_reciprocal36.73
I(0) (reciprocal space) i0_reciprocal258300000.0000
Solution quality estimate total_estimate0.9052
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary45.5
Skewness Skewness skewness0.113
Kurtosis Kurtosis kurtosis-0.570
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15870000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.905

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd4gjxa_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.169 — C-type lectin-like
Superfamily Superfamily superfamilyd.169.1 — C-type lectin-like
Family Family familyd.169.1.0 — automated matches
Domain ID domain_idd4gjxb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.169 — C-type lectin-like
Superfamily Superfamily superfamilyd.169.1 — C-type lectin-like
Family Family familyd.169.1.0 — automated matches
Domain ID domain_idd4gjxc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.169 — C-type lectin-like
Superfamily Superfamily superfamilyd.169.1 — C-type lectin-like
Family Family familyd.169.1.0 — automated matches
Domain ID domain_idd4gjxd_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.169 — C-type lectin-like
Superfamily Superfamily superfamilyd.169.1 — C-type lectin-like
Family Family familyd.169.1.0 — automated matches
Domain ID domain_idd4gjxe_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.169 — C-type lectin-like
Superfamily Superfamily superfamilyd.169.1 — C-type lectin-like
Family Family familyd.169.1.0 — automated matches
Domain ID domain_idd4gjxf_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.169 — C-type lectin-like
Superfamily Superfamily superfamilyd.169.1 — C-type lectin-like
Family Family familyd.169.1.0 — automated matches
Domain ID domain_idd4gjxg_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.169 — C-type lectin-like
Superfamily Superfamily superfamilyd.169.1 — C-type lectin-like
Family Family familyd.169.1.0 — automated matches
Domain ID domain_idd4gjxh_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.169 — C-type lectin-like
Superfamily Superfamily superfamilyd.169.1 — C-type lectin-like
Family Family familyd.169.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id4gjxA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
Domain ID domain_id4gjxB01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
Domain ID domain_id4gjxC01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
Domain ID domain_id4gjxD01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
Domain ID domain_id4gjxE01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
Domain ID domain_id4gjxF01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
Domain ID domain_id4gjxG01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
Domain ID domain_id4gjxH01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A

8. Citations (1)

9. Files and Curves (10)