8Q8J | pdb_00008q8j

Crystal structure of human GPX4-R152H

• PDB DOI: https://doi.org/10.2210/pdb8Q8J/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-08-18 Released: 2024-08-28 
• Deposition Author(s): Napolitano, V., Mourao, A., Kolonko, M., Bostock, M.J., Sattler, M., Conrad, M., Popowicz, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human GPX4-R152H

Lorenz, S.M., Wahida, A., Emler, D., Bostock, M., Seibt, T., Mourao, A., Trumbach, D., Rizzollo, F., Napolitano, V., Kolonko-Adamska, M., Sommer, J., Woo, M.S., Rothammer, N., Gaussman, S., Alves, F., Burkle, E., Wanninger, J., Boxleitner, K.M., Stadler, M., Doll, S., Mishima, E., Nakamura, T., Maida, A., Hass, D., Escamilla-Ayala, A., Puentes, L.P., Lenberg, J., Friedman, J., Scale, C., Proneth, B., Henkelmann, L., Aldrovandi, M., Agostinis, P., Zimprich, A., Vogt-Weisenhorn, D., Holter-Koch, S., Lewerenz, J., Steinacker, P., Garcia-Saez, A.J., Wurst, W., Tietze, A., Mann, M., Westmeyer, G.G., Friese, M.A., Ramesh, S.K., Wigby, K., Sattler, M., Ingold, I., Ayton, S., Jayavelu, A.K., Popowicz, G., Conrad, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 18.94 kDa 
• Atom Count: 1,420 
• Modeled Residue Count: 165 
• Deposited Residue Count: 165 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione peroxidase	A	165	Homo sapiens	Mutation(s): 1  Gene Names: GPX4 EC: 1.11.1.12 (UniProt), 1.11.1.9 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P36969 (Homo sapiens) Explore P36969  Go to UniProtKB:  P36969
PHAROS:  P36969 GTEx:  ENSG00000167468

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.871	α = 90
b = 45.048	β = 90
c = 82.954	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-28 
Deposition Author(s): Napolitano, V., Mourao, A., Kolonko, M., Bostock, M.J., Sattler, M., Conrad, M., Popowicz, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-08-28
  Type: Initial release