6ZIC

CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH 3S-HYDROXYBUTANOYL-COA AND NADH

• PDB DOI: https://doi.org/10.2210/pdb6ZIC/pdb

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


• Deposited: 2020-06-25 Released: 2021-07-07 
• Deposition Author(s): Wierenga, R.K., Sridhar, S., Kiema, T.R.
• Funding Organization(s): European Union (EU)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.234 
• R-Value Work: 0.200 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH 3S-HYDROXYBUTANOYL-COA AND NADH

Wierenga, R.K., Sridhar, S., Kiema, T.R.

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.

Macromolecule Content

• Total Structure Weight: 165.74 kDa 
• Atom Count: 11,611 
• Modelled Residue Count: 1,437 
• Deposited Residue Count: 1,484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisomal bifunctional enzyme	A [auth AAA], B [auth BBB]	742	Rattus norvegicus	Mutation(s): 0  Gene Names: Ehhadh, Mfe1 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
3HC (Subject of Investigation/LOI)	C [auth AAA], L [auth BBB]	3-HYDROXYBUTANOYL-COENZYME A C25 H42 N7 O18 P3 S QHHKKMYHDBRONY-VKBDFPRVSA-N
NAI (Subject of Investigation/LOI)	H [auth AAA], N [auth BBB]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N
SO4	K [auth AAA], O [auth BBB]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth AAA], E [auth AAA], F [auth AAA], G [auth AAA], I [auth AAA], J [auth AAA], M [auth BBB]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.234 
• R-Value Work: 0.200 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.637	α = 90
b = 127.086	β = 90
c = 227.1	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-07-07 
Deposition Author(s): Wierenga, R.K., Sridhar, S., Kiema, T.R.

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Funding Organization	Location	Grant Number
European Union (EU)	Finland	731005

Revision History  

• Version 1.0: 2021-07-07
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Derived calculations, Refinement description