7XVX | pdb_00007xvx

Neutron crystal structure of human macrophage migration inhibitory factor

PDB DOI: https://doi.org/10.2210/pdb7XVX/pdb

Classification: CYTOKINE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-05-25 Released: 2023-05-31
Deposition Author(s): Ezawa, T., Tamada, T., Odaka, M., Matsumura, H.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.169 (Depositor), 0.171 (DCC)
R-Value Work:
0.154 (Depositor), 0.156 (DCC)
R-Value Observed:
0.155 (Depositor)

Method: NEUTRON DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.200 (Depositor)
R-Value Work:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Neutron crystal structure of human macrophage migration inhibitory factor

Ezawa, T., Nakagaki, T., Sugishima, K., Ishida, T., Hirano, Y., Kusaka, K., Tamada, T., Odaka, M., Wakui, H., Matsumura, H.

To be published.

Macromolecule Content

Total Structure Weight: 37.07 kDa
Atom Count: 2,971
Modeled Residue Count: 342
Deposited Residue Count: 342
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage migration inhibitory factor	A, B, C	114	Homo sapiens	Mutation(s): 0 Gene Names: MIF, GLIF, MMIF EC: 5.3.2.1 (PDB Primary Data), 5.3.3.12 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P14174 (Homo sapiens) Explore P14174 Go to UniProtKB: P14174
PHAROS: P14174 GTEx: ENSG00000240972
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14174
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.169 (Depositor), 0.171 (DCC)
R-Value Work: 0.154 (Depositor), 0.156 (DCC)
R-Value Observed: 0.155 (Depositor)

Method: NEUTRON DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.200 (Depositor)
R-Value Work: 0.180 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.534	α = 90
b = 96.534	β = 90
c = 105.596	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-05-31

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	19K07011

Revision History (Full details and data files)

Version 1.0: 2023-05-31
Type: Initial release
Version 1.1: 2024-04-03
Changes: Data collection, Refinement description

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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.