9YYA | pdb_00009yya

Macrophage Migration Inhibitory Factor 1 from Necator Americanus

PDB DOI: https://doi.org/10.2210/pdb9YYA/pdb

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

Deposited: 2025-10-28 Released: 2025-11-12
Deposition Author(s): Orkwis, J.A., Lolis, E.J., Manjula, R.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.240 (Depositor), 0.240 (DCC)
R-Value Work:
0.198 (Depositor), 0.197 (DCC)

Starting Model: experimental
View more details

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., Manjula, R., Lolis, E.J.

To be published.

Macromolecule Content

Total Structure Weight: 155.5 kDa
Atom Count: 11,068
Modeled Residue Count: 1,407
Deposited Residue Count: 1,416
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage migration inhibitory factor	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	118	Necator americanus	Mutation(s): 0 Gene Names: Necator_chrV.g17532, NECAME_06445, RB195_012742
UniProt
Find proteins for W2TWH5 (Necator americanus) Explore W2TWH5 Go to UniProtKB: W2TWH5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	W2TWH5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.240 (Depositor), 0.240 (DCC)
R-Value Work: 0.198 (Depositor), 0.197 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.632	α = 90
b = 126.213	β = 90
c = 155.766	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-11-12
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.