6MKE

Crystal Structure of Peptidylprolyl Isomerase from Naegleria fowleri with bound FK506

• PDB DOI: https://doi.org/10.2210/pdb6MKE/pdb

• Classification: ISOMERASE
• Organism(s): Naegleria fowleri
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-09-25 Released: 2018-10-03 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.257 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 

Literature

Crystal Structure of Peptidylprolyl Isomerase from Naegleria fowleri with bound FK506

Dranow, D.M., Bertolin, B.A., Fox III, D., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 60.04 kDa 
• Atom Count: 4,254 
• Modelled Residue Count: 468 
• Deposited Residue Count: 508 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidylprolyl isomerase	A, B, C, D	127	Naegleria fowleri	Mutation(s): 0  Gene Names: NF0084240 EC: 5.2.1.8
UniProt
Find proteins for A0A2H4A315 (Naegleria fowleri) Explore A0A2H4A315  Go to UniProtKB:  A0A2H4A315

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FK5	E [auth A], F [auth B], G [auth C], H [auth D]	8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN C44 H69 N O12 QJJXYPPXXYFBGM-LFZNUXCKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.257 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/m36mke

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.05	α = 90
b = 60.16	β = 97.12
c = 73.34	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Currently 6MKE does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 2018-10-03 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2018-10-03
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description