4grq

Characterization of N- and C- terminus mutants of human MIF

Method: X-RAY DIFFRACTION Dmax: 59.7 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 Mutation:Pro1-Ala2 are insertions CL CHLORIDE ION × 6 SO4 SULFATE ION × 1 AVL 2-methyl-1-[2-(propan-2-yl)pyrazolo[1,5-a]pyridin-3-yl]propan-1-one × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;310 K;1.6M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K Resolution 1.65 Å R-free 0.161

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 1–116; UniProt 2–115 Author chain B; PDBConstruct 1–116; UniProt 2–115 Author chain C; PDBConstruct 1–116; 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 4grq

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id4grq
Deposition date deposition_date2012-08-26
Structure title titleCharacterization of N- and C- terminus mutants of human MIF
Keywords keywordsalpha/beta mixture, cytokine, Isomerase; cytokine, Isomerase
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier20.06
Radius of gyration Rg (electron density) rg_electron18.80
Forward intensity I(0) i025244800.00
Molecular weight molecular_weight38004.0 kDa
Excluded volume excluded_volume47295 ų
Envelope volume envelope_volume52889 ų
Hydration-shell volume shell_volume22627 ų
Envelope diameter envelope_diameter58.1
Shell Rg shell_rg25.99
Envelope Rg envelope_rg18.89
Shape Rg shape_rg18.81
Total Rg total_rg19.70
Total atoms total_atoms5287
Residues n_residues348
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 dmax59.7
Rg (real space) rg_real19.89
Rg uncertainty (real space) rg_real_error0.24
I(0) (real space) i0_real2.5240e+07
I(0) uncertainty (real space) i0_real_error2.8970e+05
Rg (reciprocal space) rg_reciprocal19.92
I(0) (reciprocal space) i0_reciprocal25250000.0000
Solution quality estimate total_estimate0.8230
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.4
Skewness Skewness skewness0.012
Kurtosis Kurtosis kurtosis-0.545
Angular range angular_range— – 0.3950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5879000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd4grqa_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.3 — MIF-related
Domain ID domain_idd4grqb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.3 — MIF-related
Domain ID domain_idd4grqc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.3 — MIF-related

CATH v4.4 (3 domains)

Domain ID domain_id4grqA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id4grqB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id4grqC00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor

8. Citations (1)

9. Files and Curves (10)