9YY9 | pdb_00009yy9

Macrophage Migration Inhibitory Factor 1 from Heligmosomoides polygyrus

PDB DOI: https://doi.org/10.2210/pdb9YY9/pdb

Classification: CYTOKINE
Organism(s): Heligmosomoides polygyrus
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2025-10-28 Released: 2025-11-05
Deposition Author(s): Orkwis, J.A., Lolis, E.J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free:
0.175 (Depositor), 0.175 (DCC)
R-Value Work:
0.142 (Depositor), 0.142 (DCC)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Helminth proteins recapitulate key structural motifs of MIF to facilitate immunomodulation of host receptors

Orkwis, J.A., Lolis, E.J.

To be published.

Macromolecule Content

Total Structure Weight: 12.64 kDa
Atom Count: 958
Modeled Residue Count: 117
Deposited Residue Count: 117
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage migration inhibitory factor	A	117	Heligmosomoides polygyrus	Mutation(s): 0 Gene Names: HPBE_LOCUS13691
UniProt
Find proteins for A0A183FYG9 (Heligmosomoides polygyrus) Explore A0A183FYG9 Go to UniProtKB: A0A183FYG9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A183FYG9
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.175 (Depositor), 0.175 (DCC)
R-Value Work: 0.142 (Depositor), 0.142 (DCC)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.654	α = 90
b = 71.654	β = 90
c = 73.125	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
FAST_DP	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-11-05
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.