8tt9

X-ray structure of Macrophage Migration Inhibitory Factor (MIF) Covalently Bound to 4-hydroxyphenylpyruvate (HPP)

Method: X-RAY DIFFRACTION Dmax: 59.6 Å Quality: GOOD

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

Macrophage migration inhibitory factor

Homo sapiens

UniProt P14174

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 2–115 Chain B; UniProt 2–115 Chain C; UniProt 2–115 Not recorded ENO 3-(4-HYDROXY-PHENYL)PYRUVIC ACID × 3 IPA ISOPROPYL ALCOHOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;2M AMMONIUM SULFATE, 4% ISOPROPANOL, 0.1 M TRIS(HYDROXYMETHYL)AMINOMETHAN; MIXED WITH PROTEIN:INHIBITOR COMPLEX IN A 1:10 RATIO Resolution 1.68 Å R-free 0.199

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.

117 other PDB entries and 132 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MIF_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–114; UniProt 2–115 Author chain B; PDBConstruct 1–114; UniProt 2–115 Author chain C; PDBConstruct 1–114; UniProt 2–115

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 8tt9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8tt9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8tt9
Deposition date deposition_date2023-08-13
Structure title titleX-ray structure of Macrophage Migration Inhibitory Factor (MIF) Covalently Bound to 4-hydroxyphenylpyruvate (HPP)
Keywords keywordsMACROPHAGE MIGRATION INHIBITORY FACTOR, CYTOKINE; CYTOKINE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier19.86
Radius of gyration Rg (electron density) rg_electron18.65
Forward intensity I(0) i022988900.00
Molecular weight molecular_weight37134.0 kDa
Excluded volume excluded_volume46548 ų
Envelope volume envelope_volume51662 ų
Hydration-shell volume shell_volume22305 ų
Envelope diameter envelope_diameter56.9
Shell Rg shell_rg25.76
Envelope Rg envelope_rg18.70
Shape Rg shape_rg18.67
Total Rg total_rg19.50
Total atoms total_atoms2610
Residues n_residues342
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 dmax59.6
Rg (real space) rg_real19.66
Rg uncertainty (real space) rg_real_error0.34
I(0) (real space) i0_real2.2990e+07
I(0) uncertainty (real space) i0_real_error2.7060e+05
Rg (reciprocal space) rg_reciprocal19.69
I(0) (reciprocal space) i0_reciprocal22990000.0000
Solution quality estimate total_estimate0.8948
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.9
Skewness Skewness skewness-0.005
Kurtosis Kurtosis kurtosis-0.559
Angular range angular_range— – 0.4000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4873000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.888; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.998

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)