5OMO

CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH WITH 3S-HYDROXY-DECANOYL-COA AND 3-KETO-DECANOYL-COA

• PDB DOI: https://doi.org/10.2210/pdb5OMO/pdb
• Entry: 5OMO supersedes: 5AAJ

• Classification: OXIDOREDUCTASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-08-01 Released: 2017-09-06 
• Deposition Author(s): Kasaragod, P., Kiema, T.-R., Schmitz, W., Hiltunen, J.K., Wierenga, R.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.228 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE 1 (RPMFE1) COMPLEXED WITH 3S-HYDROXY-DECANOYL-COA AND 3- KETO-DECANOYL-COA

Kasaragod, P., Balcha, G., Sridhar, S., Schmitz, W., Kiema, T.-R., Hiltunen, J.K., Wierenga, R.K.

Not 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.

Macromolecule Content

• Total Structure Weight: 165.52 kDa 
• Atom Count: 11,586 
• Modelled Residue Count: 1,443 
• Deposited Residue Count: 1,484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisomal bifunctional enzyme	A, B	742	Rattus norvegicus	Mutation(s): 0  Gene Names: Ehhadh EC: 4.2.1.17 (PDB Primary Data), 5.3.3.8 (PDB Primary Data), 1.1.1.35 (PDB Primary Data)
UniProt
Find proteins for P07896 (Rattus norvegicus) Explore P07896  Go to UniProtKB:  P07896

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZOZ (Subject of Investigation/LOI)	I [auth A]	3-KETO-DECANOYL-COA C31 H52 N7 O18 P3 S AZCVXMAPLHSIKY-HSJNEKGZSA-N
HSC (Subject of Investigation/LOI)	H [auth A], N [auth B]	(S)-3-HYDROXYDECANOYL-COA C31 H50 N7 O18 P3 S HIVSMYZAMUNFKZ-PNPVFPMQSA-J
SO4	C [auth A], D [auth A], E [auth A], J [auth B], K [auth B], L [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], G [auth A], M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.228 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.96	α = 90
b = 125.08	β = 90
c = 223.53	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-06 
Deposition Author(s): Kasaragod, P., Kiema, T.-R., Schmitz, W., Hiltunen, J.K., Wierenga, R.K.
• This entry supersedes: 5AAJ

Revision History  

• Version 1.0: 2017-09-06
  Type: Initial release
  
• Version 1.1: 2018-05-02
  Changes: Data collection
• Version 1.2: 2019-03-20
  Changes: Data collection, Database references
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Refinement description