8VQP | pdb_00008vqp

Crystal Structure Analysis of EGR1-MIDN

PDB DOI: https://doi.org/10.2210/pdb8VQP/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-01-18 Released: 2025-07-23
Deposition Author(s): Seo, H.-S., Dhe-Paganon, S.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free:
0.271 (Depositor), 0.275 (DCC)
R-Value Work:
0.244 (Depositor), 0.249 (DCC)
R-Value Observed:
0.245 (Depositor)

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

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

Literature

Crystal Structure Analysis of EGR1-MIDN

Seo, H.-S., Dhe-Paganon, S.

To be published.

Macromolecule Content

Total Structure Weight: 16.54 kDa
Atom Count: 900
Modeled Residue Count: 119
Deposited Residue Count: 154
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EGR1-MIDN	A	154	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q504T8 (Homo sapiens) Explore Q504T8 Go to UniProtKB: Q504T8
PHAROS: Q504T8 GTEx: ENSG00000167470
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q504T8
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free: 0.271 (Depositor), 0.275 (DCC)
R-Value Work: 0.244 (Depositor), 0.249 (DCC)
R-Value Observed: 0.245 (Depositor)

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.46	α = 90
b = 70.06	β = 90
c = 84.78	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
xia2	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-23

Deposition Author(s):

Dhe-Paganon, S.

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2025-07-23
Type: Initial release

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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.