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)

Experimental Data Snapshot

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

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

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

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07896
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3HC (Subject of Investigation/LOI) Query on 3HC Download Ideal Coordinates CCD File SDF format, chain C [auth AAA] SDF format, chain L [auth BBB] MOL2 format, chain C [auth AAA] MOL2 format, chain L [auth BBB] mmCIF format, chain C [auth AAA] mmCIF format, chain L [auth BBB]	C [auth AAA], L [auth BBB]	3-HYDROXYBUTANOYL-COENZYME A C₂₅ H₄₂ N₇ O₁₈ P₃ S QHHKKMYHDBRONY-VKBDFPRVSA-N		Interactions Focus chain C [auth AAA] Focus chain L [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain L [auth BBB]
NAI (Subject of Investigation/LOI) Query on NAI Download Ideal Coordinates CCD File SDF format, chain H [auth AAA] SDF format, chain N [auth BBB] MOL2 format, chain H [auth AAA] MOL2 format, chain N [auth BBB] mmCIF format, chain H [auth AAA] mmCIF format, chain N [auth BBB]	H [auth AAA], N [auth BBB]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain H [auth AAA] Focus chain N [auth BBB] Interactions & Density Focus chain H [auth AAA] Focus chain N [auth BBB]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain K [auth AAA] SDF format, chain O [auth BBB] MOL2 format, chain K [auth AAA] MOL2 format, chain O [auth BBB] mmCIF format, chain K [auth AAA] mmCIF format, chain O [auth BBB]	K [auth AAA], O [auth BBB]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth AAA] Focus chain O [auth BBB] Interactions & Density Focus chain K [auth AAA] Focus chain O [auth BBB]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth AAA] SDF format, chain E [auth AAA] SDF format, chain F [auth AAA] SDF format, chain G [auth AAA] SDF format, chain I [auth AAA] SDF format, chain J [auth AAA] SDF format, chain M [auth BBB] MOL2 format, chain D [auth AAA] MOL2 format, chain E [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain J [auth AAA] MOL2 format, chain M [auth BBB] mmCIF format, chain D [auth AAA] mmCIF format, chain E [auth AAA] mmCIF format, chain F [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain I [auth AAA] mmCIF format, chain J [auth AAA] mmCIF format, chain M [auth BBB]	D [auth AAA] E [auth AAA] F [auth AAA] G [auth AAA] I [auth AAA] 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		Interactions Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain M [auth BBB] Interactions & Density Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain M [auth BBB]

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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-07-07

Deposition Author(s):

Wierenga, R.K.

Sridhar, S.

Kiema, T.R.

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

Revision History (Full details and data files)

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