4EKZ

Crystal structure of reduced hPDI (abb'xa')

• PDB DOI: https://doi.org/10.2210/pdb4EKZ/pdb

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


• Deposited: 2012-04-10 Released: 2013-04-10 
• Deposition Author(s): Wang, C., Li, W., Ren, J., Ke, H., Gong, W., Feng, W., Wang, C.-C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.250 
• R-Value Work: 0.236 
• R-Value Observed: 0.237 

Literature

Structural insights into the redox-regulated dynamic conformations of human protein disulfide isomerase

Wang, C., Li, W., Ren, J., Fang, J., Ke, H., Gong, W., Feng, W., Wang, C.-C.

(2013) Antioxid Redox Signal 19: 44-53

• PubMed: 22657537 
• DOI: https://doi.org/10.1089/ars.2012.4630
• Primary Citation of Related Structures:  
  4EKZ, 4EL1


• PubMed Abstract: 
  

  Human protein disulfide isomerase (hPDI) is a key enzyme and a redox-regulated chaperone responsible for oxidative protein folding in the endoplasmic reticulum. This work aims to reveal the molecular mechanism underlying the redox-regulated functions of hPDI by determining the crystal structures of hPDI in different redox states.

---

Organizational Affiliation: 

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

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: 54.2 kDa 
• Atom Count: 3,799 
• Modelled Residue Count: 469 
• Deposited Residue Count: 482 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein disulfide-isomerase	A	482	Homo sapiens	Mutation(s): 0  Gene Names: P4HB, ERBA2L, PDI, PDIA1, PO4DB EC: 5.3.4.1
UniProt & NIH Common Fund Data Resources
Find proteins for P07237 (Homo sapiens) Explore P07237  Go to UniProtKB:  P07237
PHAROS:  P07237 GTEx:  ENSG00000185624

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.250 
• R-Value Work: 0.236 
• R-Value Observed: 0.237 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.453	α = 90
b = 100.586	β = 90
c = 123.767	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-10 
Deposition Author(s): Wang, C., Li, W., Ren, J., Ke, H., Gong, W., Feng, W., Wang, C.-C.

Revision History  

• Version 1.0: 2013-04-10
  Type: Initial release
  
• Version 1.1: 2013-07-03
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description