9yiu

Macrophage Migration Inhibitory Factor 2 from Necator americanus

Method: X-RAY DIFFRACTION D_max: 50.4 Å Quality: GOOD

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

L-dopachrome isomerase

Necator americanus

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 G； UniProt 2–115	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293.15 K；1.26 M NaH2PO4 (Precipitant), 0.14 M K2HPO4 (Precipitant)	Resolution 1.73 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.

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

View Construct and Data Evidence

UniProt name	W2TK26_NECAM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain G； 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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9yiu
Deposition date deposition_date	2025-10-02
Structure title title	Macrophage Migration Inhibitory Factor 2 from Necator americanus
Keywords keywords	MIF, helminth, orthologue, parasite, CYTOKINE, ISOMERASE; ISOMERASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	15.75 Å
Radius of gyration Rg (electron density) rg_electron	14.30 Å
Forward intensity I(0) i0	2925670.00
Molecular weight molecular_weight	11985.0 kDa
Excluded volume excluded_volume	15042 Å³
Envelope volume envelope_volume	17498 Å³
Hydration-shell volume shell_volume	10916 Å³
Envelope diameter envelope_diameter	49.5 Å
Shell Rg shell_rg	19.30 Å
Envelope Rg envelope_rg	14.60 Å
Shape Rg shape_rg	14.32 Å
Total Rg total_rg	15.33 Å
Total atoms total_atoms	1690
Residues n_residues	114
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	50.4 Å
Rg (real space) rg_real	15.70 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	2.9260e+06
I(0) uncertainty (real space) i0_real_error	2.9430e+04
Rg (reciprocal space) rg_reciprocal	15.71 Å
I(0) (reciprocal space) i0_reciprocal	2926000.0000
Solution quality estimate total_estimate	0.8959
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.9 Å
Skewness Skewness skewness	0.227
Kurtosis Kurtosis kurtosis	-0.385
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	325700.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.978

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	64.653 Å
Unit-cell length b length_b	64.653 Å
Unit-cell length c length_c	174.687 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	1.726 Å
Low-resolution limit resolution_low	29.115 Å
R factor r_factor	—
R_work r_work	0.1912
R_free r_free	0.2088

Description description	L-dopachrome isomerase
Molecular weight formula_weight	12205.8 kDa
EC 编号 ec_number	5.3.2.1,5.3.3.12
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	G
Atom count atom_count	1715

Macrophage Migration Inhibitory Factor 2 from Necator americanus

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

L-dopachrome isomerase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Necator americanus
通用名 common_name	New World hookworm
NCBI Class编号 ncbi_taxonomy_id	51031
宿主生物 host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	25

fit	/app/data/saxs_computation/yi/9yiu/9yiu.fit
pddf	/app/data/pr_computation/yi/9yiu/9yiu.pr.out
profile	/app/data/saxs_computation/yi/9yiu/9yiu.dat