9yy9

Macrophage Migration Inhibitory Factor 1 from Heligmosomoides polygyrus

Method: X-RAY DIFFRACTION Dmax: 53.3 Å Quality: GOOD

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

Macrophage migration inhibitory factor

Heligmosomoides polygyrus

UniProt A0A183FYG9

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 2–118 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;298.15 K;0.1 M Na Acet 4.5 pH (Buffer), 25 %w/v PEG 3350 (Precipitant) Resolution 1.62 Å R-free 0.175

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A0A183FYG9_HELPZ
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–117; UniProt 2–118

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 9yy9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9yy9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9yy9
Deposition date deposition_date2025-10-28
最后修订 last_revision2025-11-05
Structure title titleMacrophage Migration Inhibitory Factor 1 from Heligmosomoides polygyrus
Keywords keywordsorthologue, parasite, helminth, cytokine; CYTOKINE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier15.86
Radius of gyration Rg (electron density) rg_electron14.62
Forward intensity I(0) i03171510.00
Molecular weight molecular_weight12611.0 kDa
Excluded volume excluded_volume15895 ų
Envelope volume envelope_volume18189 ų
Hydration-shell volume shell_volume11167 ų
Envelope diameter envelope_diameter52.0
Shell Rg shell_rg19.58
Envelope Rg envelope_rg14.94
Shape Rg shape_rg14.63
Total Rg total_rg15.66
Total atoms total_atoms1803
Residues n_residues117
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 dmax53.3
Rg (real space) rg_real15.84
Rg uncertainty (real space) rg_real_error0.37
I(0) (real space) i0_real3.1720e+06
I(0) uncertainty (real space) i0_real_error3.8800e+04
Rg (reciprocal space) rg_reciprocal15.84
I(0) (reciprocal space) i0_reciprocal3172000.0000
Solution quality estimate total_estimate0.8763
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary18.9
Skewness Skewness skewness0.301
Kurtosis Kurtosis kurtosis-0.285
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha417900.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.823; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.938

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

8. Citations (1)

9. Files and Curves (10)