4EF0 | pdb_00004ef0

Crystal Structure of the first catalytic domain of protein disulfide isomerase P5

• PDB DOI: https://doi.org/10.2210/pdb4EF0/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-03-28 Released: 2013-04-03 
• Deposition Author(s): Vinaik, R., Kozlov, G., Gehring, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the first catalytic domain of protein disulfide isomerase P5

Vinaik, R., Kozlov, G., Gehring, K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 27.6 kDa 
• Atom Count: 2,181 
• Modeled Residue Count: 230 
• Deposited Residue Count: 246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein disulfide-isomerase A6	A, B	123	Homo sapiens	Mutation(s): 0  Gene Names: PDIA6, ERP5, P5, TXNDC7 EC: 5.3.4.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15084 (Homo sapiens) Explore Q15084  Go to UniProtKB:  Q15084
PHAROS:  Q15084 GTEx:  ENSG00000143870

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.852	α = 90
b = 129.852	β = 90
c = 45.226	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-03 
Deposition Author(s): Vinaik, R., Kozlov, G., Gehring, K.

Revision History  

• Version 1.0: 2013-04-03
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Refinement description